io.github.genmnz/jean

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Au dernier audit MCP Hub, le serveur MCP « io.github.genmnz/jean » est classé « Non encore testé ». Référencé dans l'annuaire. Seul le pentest comportemental fait foi, et il n'a pas encore été exécuté sur ce serveur. Le verdict est réévalué en continu ; consultez la fiche pour l'état à jour.

Méthode : MCP Hub analyse la description de chaque outil (couche 1) et, pour le verdict fort, exécute le serveur dans une micro-VM isolée avec leurres et réseau bloqué (couche 2). On publie des noms et des compteurs, jamais le contenu brut renvoyé par un outil.

Les 289 outils

• activity_cliffs≈ 572 tokens

  SALI activity cliffs (Guha & Van Drie 2008) in a list of small molecules with one activity each: every pair scored as the activity difference over one minus the Tanimoto similarity of RDKit path fingerprints, steepest first; identical fingerprints with different activities score Infinity. Indices are 0-based.

  Paramètres, retour & exemple (5)

  Paramètres

  • scale · string · optionnel · pIc50Um | asGiven
    how the activities are read. Values: pIc50Um (pIC50 from a µM IC50), asGiven (As given).
  • _files · array · optionnel
    The project: record references shaped like _subject. Their records become library documents a tool names in sequences/parts/document; a trace or alignment is found by file name.
  • _subject · object · optionnel
    The record to act on: exactly one of sequence, accession (+source), sample (an id from list_samples) or file ({name, text} or {name, base64}); record_index picks one record of several.
  • molecules · array · requis
    the structures: one SMILES or molfile per entry.
  • activities · array · requis
    one number per structure, in the same order; a non-number leaves it out.

  Exemple d'appel

  {"name": "activity_cliffs", "arguments": {"molecules": [], "activities": []}}

  Exemple de retour

  {"content": [{"type": "text", "text": "…"}], "structuredContent": {"pairs": "texte", "summary": "texte"}}

• adopt_trace_calls≈ 882 tokens

  Replace a Sanger read's own base calls with TraceTuner's, on the trace that is open, so the rest of the editor works from the re-called read: its sequence, its consensus, its verification against a reference, and every export. The signal is untouched — this is the same electropherogram with a second opinion about where the bases are — and every coordinate already on the read is carried across the peaks it sits on, so a trim window, a hand-corrected call and an annotation all follow. Reports what moved and what could not be placed. Use `call_bases_from_trace` instead to ASK what the re-call says without changing the read.

  Paramètres, retour & exemple (5)

  Paramètres

  • mode · string · optionnel · rescore | denovo | het | mix
    which reading to adopt. `rescore` keeps the instrument's bases and only re-measures their confidence; `denovo` derives the bases from the signal and can return a different read LENGTH; `het` and `mix` derive them and write a two-base IUB code where a second allele is present, differing only in whether the two are assumed equal in amount.
  • table · string · optionnel · 3700pop5 | 3700pop6 | 3100pop6 | 3730pop7
    the instrument and polymer the quality scale was calibrated on. There is no universal default: a base scores differently under a different table.
  • _files · array · optionnel
    The project: record references shaped like _subject. Their records become library documents a tool names in sequences/parts/document; a trace or alignment is found by file name.
  • _subject · object · optionnel
    The record to act on: exactly one of sequence, accession (+source), sample (an id from list_samples) or file ({name, text} or {name, base64}); record_index picks one record of several.
  • min_ratio · number · optionnel
    for `het` and `mix` only: how tall a second peak must be, as a fraction of the called one, to be called as a second allele. Ignored by the other two modes. Only applies when mode is het or mix.

  Exemple d'appel

  {"name": "adopt_trace_calls", "arguments": {"mode": "rescore", "table": "3700pop5", "_files": [], "_subject": {}, "min_ratio": 1}}

  Exemple de retour

  {"content": [{"type": "text", "text": "…"}], "structuredContent": {"bases": 1, "sequence": "texte", "basesBefore": 1, "everythingPlaced": true}}

• align_read≈ 680 tokens

  Pairwise-align ONE sequencing read against a reference and hand on the two gapped rows, so the read can be graded. Needleman-Wunsch with free end gaps and the IUPAC substitution matrix — SeqTrace's aligner, the same call the trace editor makes, so a pipeline and the panel align a read identically. Leave `reference` unset to align against the record this step runs on.

  Paramètres, retour & exemple (4)

  Paramètres

  • read · string · requis
    the read's bases — wire a trace reader's `sequence` output here, or paste them.
  • _files · array · optionnel
    The project: record references shaped like _subject. Their records become library documents a tool names in sequences/parts/document; a trace or alignment is found by file name.
  • _subject · object · optionnel
    The record to act on: exactly one of sequence, accession (+source), sample (an id from list_samples) or file ({name, text} or {name, base64}); record_index picks one record of several.
  • reference · string · optionnel
    what to align against. Unset, it is the record this step runs on (the open plasmid, or an upstream product wired into the subject).

  Exemple d'appel

  {"name": "align_read", "arguments": {"read": "texte"}}

  Exemple de retour

  {"content": [{"type": "text", "text": "…"}], "structuredContent": {"columns": 1, "identity": 1, "mismatches": 1, "alignedRead": "texte", "referenceLength": 1, "alignedReference": "texte"}}

• align_sequences≈ 2160 tokens

  Multiple-sequence alignment over several sequences, under either of TWO engines that answer different questions and neither of which is a fallback for the other. `poa` (partial-order, poapy) aligns into a graph, keeps every path a read took and produces its own consensus row — what a pile of reads over one locus wants. `progressive` (biotite) computes Feng-Doolittle distances, clusters them into a guide tree and merges along it under "once a gap, always a gap" — the classic MSA algorithm, what a FAMILY of homologous genes wants, and what a reader coming from Clustal or MUSCLE expects. Wire many upstream `record`/`sequence` outputs into `sequences`, or name library documents.

  Paramètres, retour & exemple (17)

  Paramètres

  • gap · number · optionnel
    `poa` only: score for a gap column. Negative. Only applies when engine is poa. Advanced.
  • match · number · optionnel
    `poa` only: score for a pair of identical symbols. Only applies when engine is poa. Advanced.
  • _files · array · optionnel
    The project: record references shaped like _subject. Their records become library documents a tool names in sequences/parts/document; a trace or alignment is found by file name.
  • engine · string · optionnel · poa | progressive
    which aligner builds the alignment. They answer DIFFERENT questions: `poa` keeps every path through a pile of reads and emits its own consensus row, `progressive` merges a family along a guide tree the way Clustal and MUSCLE do. Each engine reads only its own parameters below. Values: poa (Partial-order (poapy) - reads over one locus), progressive (Progressive (biotite) - a family, guide-tree merged).
  • _subject · object · optionnel
    The record to act on: exactly one of sequence, accession (+source), sample (an id from list_samples) or file ({name, text} or {name, base64}); record_index picks one record of several.
  • gap_open · number · optionnel
    `progressive`, affine only: the penalty for STARTING a gap. Negative. Only applies when affine_gap is true.
  • mismatch · number · optionnel
    `poa` only: score for a mismatching pair. Negative. Only applies when engine is poa. Advanced.
  • sequences · array · optionnel
    the sequences to align — wire several upstream outputs here, or list library document names/ids.
  • affine_gap · boolean · optionnel
    `progressive` only: `false` charges one flat penalty per gap column; `true` charges separate opening and extension penalties, which is what keeps a real indel as ONE gap instead of many. Only applies when engine is progressive.
  • gap_extend · number · optionnel
    `progressive`, affine only: the penalty for each column a gap is extended by. Negative, and gentler than `gap_open` - an extension harsher than the opening makes the aligner prefer many short gaps to one long indel. Only applies when affine_gap is true.
  • guide_tree · string · optionnel · upgma | nj | bionj | wpgma
    `progressive` only: which tree the merge follows. The Feng-Doolittle distances are the aligner's either way; this chooses only how they are clustered into an order. UPGMA is biotite's own and the one the port reproduces byte-for-byte; neighbour-joining and BIONJ do not assume a molecular clock, so on sequences evolving at different rates they group by relatedness where UPGMA groups by raw similarity - which is exactly the case where the guide tree changes the alignment. Values: upgma (UPGMA (biotite's own)), nj (Neighbour-joining), bionj (BIONJ), wpgma (WPGMA). Only applies when engine is progressive.
  • gap_penalty · number · optionnel
    `progressive` only: the flat penalty per gap column. Negative. Only applies when affine_gap is false.
  • align_matrix · string · optionnel · auto | EDNAFULL | BLOSUM62
    `progressive` only: the substitution matrix the ALIGNMENT itself is scored with - distinct from `score_matrix`, which only scores the quality report afterwards. `auto` reads the alphabet: EDNAFULL for nucleotides, BLOSUM62 for protein. Naming the wrong one is not an error the engine can raise - BLOSUM62 reads A, C, G and T as alanine, cysteine, glycine and threonine and returns a number. Values: auto (Auto - from the alignment's alphabet), EDNAFULL (EDNAFULL - nucleotides (EMBOSS NUC.4.4)), BLOSUM62 (BLOSUM62 - amino acids). Only applies when engine is progressive.
  • global_align · boolean · optionnel
    global alignment rather than local. Poapy's own default is LOCAL; both this tool and the MSA inspector open on global, which is the choice a full-length comparison wants - switch it off for reads over part of a locus. Only applies when engine is poa. Advanced.
  • score_matrix · string · optionnel · PAM250 | BLOSUM62 | EDNAFULL
    substitution matrix for the pyMSA sum-of-pairs and star scores in the quality report. Both engines. Left unset only the matrix-free scores are computed (entropy, % non-gaps, % totally conserved columns) - an honest absence rather than a score under a matrix that does not match the alphabet. Values: PAM250 (PAM250 - amino acids, greater evolutionary distance), BLOSUM62 (BLOSUM62 - amino acids), EDNAFULL (EDNAFULL - nucleotides). Advanced.
  • include_subject · boolean · optionnel
    also align the node's subject (the open or wired record).
  • terminal_penalty · boolean · optionnel
    `progressive` only: `true` charges overhanging ends like an internal gap - right for full-length homologues. `false` makes them free, which is right when a sequence covers only part of the region, e.g. a read against a gene. Only applies when engine is progressive.

  Exemple d'appel

  {"name": "align_sequences", "arguments": {"gap": 1, "match": 1, "_files": [], "engine": "poa", "_subject": {}, "gap_open": 1}}

  Exemple de retour

  {"content": [{"type": "text", "text": "…"}], "structuredContent": {"fit": "texte", "rows": "texte", "count": 1, "engine": "texte", "length": 1, "scores": "texte", "consensus": "texte", "conservation": "texte", "guideTreeNewick": "texte", "alignedSequences": []}}

• alignment_agreement≈ 1204 tokens

  Read an alignment window and say how well its reads agree with the reference underneath them, the way the pileup's own bar does: the compared and differing base counts, plus the RefSeq gene models and known dbSNP variants over the same window. The reference is a FASTA in this project or a public UCSC assembly, exactly as the panel offers it. There is no threshold and no verdict: a rate in the tens of percent almost always means the reads were aligned to a different assembly than the one asked for, and when the file declares its own reference length the answer says so as a fact rather than as a judgement.

  Paramètres, retour & exemple (7)

  Paramètres

  • locus · string · optionnel
    the window, as a locus string (`chrM:3,300-3,460`). Unset, it is the whole of the alignment's first reference — the window the panel opens on.
  • _files · array · optionnel
    The project: record references shaped like _subject. Their records become library documents a tool names in sequences/parts/document; a trace or alignment is found by file name.
  • _subject · object · optionnel
    The record to act on: exactly one of sequence, accession (+source), sample (an id from list_samples) or file ({name, text} or {name, base64}); record_index picks one record of several.
  • variants · boolean · optionnel
    also report the known dbSNP variants in the window. Off by default, as in the panel: it is a third layer over the reads and a dense window can hold thousands.
  • alignment · string · optionnel
    which BAM or SAM in this project, by name. Unset, it is the project's only alignment — and it refuses rather than guessing when there is more than one.
  • reference · string · optionnel
    what to compare against: a FASTA in this project by name, or a UCSC assembly id (`hg38`, `hg19`, `mm39` — the same list the panel's picker fetches). Unset is the panel's own default, No reference, and then only the window and its annotation are reported.
  • gene_track · string · optionnel · ncbiRefSeqSelect | ncbiRefSeqCurated | ncbiRefSeq | ncbiRefSeqPredicted
    which NCBI RefSeq set the gene models come from. Only meaningful against a UCSC assembly. The default is one curated transcript per protein-coding gene, which carries no mitochondrial genes at all — RefSeq Curated does. Values: ncbiRefSeqSelect (RefSeq Select and MANE), ncbiRefSeqCurated (RefSeq Curated), ncbiRefSeq (RefSeq All), ncbiRefSeqPredicted (RefSeq Predicted).

  Exemple d'appel

  {"name": "alignment_agreement", "arguments": {"locus": "texte", "_files": [], "_subject": {}, "variants": true, "alignment": "texte", "reference": "texte"}}

  Exemple de retour

  {"content": [{"type": "text", "text": "…"}], "structuredContent": {"rate": 1, "genes": "texte", "reads": 1, "noCall": 1, "window": "texte", "cautions": "texte", "compared": 1, "variants": "texte", "conclusion": "texte", "mismatched": 1, "pathogenic": 1}}

• alignment_window≈ 1024 tokens

  Read one window of a BAM or SAM in this project: its reads, the depth across it, and what the pairs say about the library — the same window, filters and record cap the pileup draws. Wire `reads` into an alignment or a screen the way the pane's own hand-offs do.

  Paramètres, retour & exemple (9)

  Paramètres

  • locus · string · optionnel
    the window, as a locus string (`ctgA:1-50,001`). Unset, it is the whole of the alignment's first reference — the window the panel opens on.
  • _files · array · optionnel
    The project: record references shaped like _subject. Their records become library documents a tool names in sequences/parts/document; a trace or alignment is found by file name.
  • _subject · object · optionnel
    The record to act on: exactly one of sequence, accession (+source), sample (an id from list_samples) or file ({name, text} or {name, base64}); record_index picks one record of several.
  • min_mapq · number · optionnel
    hide reads below this mapping quality, as the pane’s Filter reads operation does. The reads are still counted — `hidden` says how many this removed.
  • alignment · string · optionnel
    which BAM or SAM in this project, by name. Unset, it is the project's only alignment — and it refuses rather than guessing when there is more than one.
  • max_reads · number · optionnel
    the record cap. More reads than this overlap the window and the result is an even SAMPLE of them, with `sampled` saying so — the pane’s own cap is the default.
  • hide_secondary · boolean · optionnel
    drop secondary alignments (FLAG 0x100).
  • hide_duplicates · boolean · optionnel
    drop reads marked as PCR or optical duplicates (FLAG 0x400).
  • hide_supplementary · boolean · optionnel
    drop supplementary alignments (FLAG 0x800).

  Exemple d'appel

  {"name": "alignment_window", "arguments": {"locus": "texte", "_files": [], "_subject": {}, "min_mapq": 1, "alignment": "texte", "max_reads": 1}}

  Exemple de retour

  {"content": [{"type": "text", "text": "…"}], "structuredContent": {"reads": "texte", "hidden": 1, "window": "texte", "sampled": true, "coverage": "texte", "depth_max": 1, "depth_mean": 1, "read_count": 1, "insert_size": "texte"}}

• analyze_melt_curves≈ 2662 tokens

  Melt curves to melting temperature, under any of THREE engines that answer different questions and none of which is a fallback for another. `plate` (RDML-Python) normalises, derives twice, calls the peaks of -dF/dT and CLASSIFIES them against the target's expected Tm into per-reaction verdicts — one peak in the window is the product, an extra peak is an artifact or a primer dimer, no peak at all is a reaction that did not amplify; it is the only engine that produces a verdict. `vertex` (MBmca diffQ) fits a quadratic near the extremum and reports its vertex, so the Tm is NOT one of the sampled temperatures — the only sub-grid answer. `curve` (qpcR) does no plate normalisation and gives no verdicts, but reports every melting peak with the AREA under it. Replicate spread travels with all three, because it describes the readings rather than the method.

  Paramètres, retour & exemple (29)

  Paramètres

  • _files · array · optionnel
    The project: record references shaped like _subject. Their records become library documents a tool names in sequences/parts/document; a trace or alignment is found by file name.
  • engine · string · optionnel · plate | vertex | curve
    which of the three engines runs. They answer DIFFERENT questions: `plate` is the only one that produces a verdict, `vertex` the only one whose Tm is not a sampled temperature, `curve` the only one that reports peak areas. Values: plate (Plate (RDML-Python) - normalise, classify, verdicts), vertex (Vertex (MBmca diffQ) - sub-grid Tm), curve (Per curve (qpcR) - peak areas).
  • _subject · object · optionnel
    The record to act on: exactly one of sequence, accession (+source), sample (an id from list_samples) or file ({name, text} or {name, base64}); record_index picks one record of several.
  • cut_area · number · optionnel
    `curve` only: drop peaks whose area is under this fraction of the largest. 0 keeps every peak, which is upstream's own default. Only applies when engine is curve. Advanced.
  • extremum · string · optionnel · auto | min | max
    `vertex` only: which extremum the melt sits at. `auto` reads each curve's direction, because upstream assumes a signal that RISES with temperature and a solution-phase melt FALLS — on which the default walks to the far end of the curve and returns a plausible-looking wrong Tm. Only applies when engine is vertex.
  • resample · boolean · optionnel
    `vertex` only: resample the curve onto an even temperature grid before differentiating. Only applies when engine is vertex. Advanced.
  • all_peaks · boolean · optionnel
    `vertex` only: report every peak the curve carries, not the dominant one alone. Only applies when engine is vertex. Advanced.
  • melt_table · string · requis
    the melt table: a header row, first column the temperature and every other column one reaction's fluorescence. The same table the Melt tab takes.
  • span_peaks · number · optionnel
    `curve` only: the span Friedman's super smoother uses when the peaks are called. Only applies when engine is curve. Advanced.
  • expected_tm · number · optionnel
    the product's expected melting temperature, which is what turns a peak list into a verdict. Left unset, every peak is reported and none is classified - an honest absence rather than a guess. Read by the `plate` engine only, because it is the only one that classifies. In C. Only applies when engine is plate.
  • norm_method · string · optionnel · exponential | bilinear | combined
    `plate` only: how each curve is normalised before it is derived. Only applies when engine is plate. Advanced.
  • peak_cutoff · number · optionnel
    `plate` only: the height a candidate must reach, as a percentage of the largest peak. In %. Only applies when engine is plate. Advanced.
  • span_smooth · number · optionnel
    `curve` only: the smoothing span of the cubic spline fitted before the analytic derivative. Only applies when engine is curve. Advanced.
  • fluor_source · string · optionnel · normalised | smooth
    `plate` only: which matrix a peak's fluorescence drop is read from — the normalised curve or the smoothed raw one. Only applies when engine is plate. Advanced.
  • expo_low_temp · number · optionnel
    `plate` only: low end of the window the EXPONENTIAL background is fitted over. In C. Only applies when norm_method is exponential or combined. Advanced.
  • peak_low_temp · number · optionnel
    `plate` only: lowest temperature a peak is looked for at. In C. Only applies when engine is plate. Advanced.
  • expo_high_temp · number · optionnel
    `plate` only: high end of the exponential fit window. In C. Only applies when norm_method is exponential or combined. Advanced.
  • peak_high_temp · number · optionnel
    `plate` only: highest temperature a peak is looked for at. In C. Only applies when engine is plate. Advanced.
  • peak_max_width · number · optionnel
    `plate` only: widest a peak may be before it is not read as one product. In C. Only applies when engine is plate. Advanced.
  • window_ceiling · number · optionnel
    `vertex` only: the largest neighbourhood half-width the quadratic is tried at. Every width from 2 up to this is fitted and the one with the best adjusted R-squared wins, so the Tm arrives with the fit quality that chose it. Only applies when engine is vertex.
  • true_peak_width · number · optionnel
    `plate` only: half-width of the window around `expected_tm` a peak must fall in to count as the product. In C. Only applies when engine is plate. Advanced.
  • replicate_robust · boolean · optionnel
    replicate spread as median and MAD rather than mean and SD. Engine-independent: it describes the readings, so every run carries it. Advanced.
  • replicate_percent · boolean · optionnel
    report replicate spread as a PERCENTAGE of the mean rather than in degrees. Advanced.
  • second_derivative · boolean · optionnel
    `vertex` only: locate the inflection points of the melt (diffQ2) rather than the peak of the first derivative. Only applies when engine is vertex. Advanced.
  • artifact_peak_width · number · optionnel
    `plate` only: half-width used when an extra peak is measured as an artifact. In C. Only applies when engine is plate. Advanced.
  • bilin_low_stop_temp · number · optionnel
    `plate` only: end of the low seed window. In C. Only applies when norm_method is bilinear or combined. Advanced.
  • bilin_high_stop_temp · number · optionnel
    `plate` only: end of the high seed window — same narrow effect as its start, for the same reproduced reason. In C. Only applies when norm_method is bilinear or combined. Advanced.
  • bilin_low_start_temp · number · optionnel
    `plate` only: start of the LOW seed window the bilinear background is fitted from. In C. Only applies when norm_method is bilinear or combined. Advanced.
  • bilin_high_start_temp · number · optionnel
    `plate` only: start of the high seed window. NARROWER THAN IT LOOKS, and upstream's own quirk reproduced: the high baseline scan walks a hard-coded 90-91 C seed, so this knob feeds ONLY the first exponential-free fit and moves the result far less than the low window does. The windows actually chosen come back in the result. In C. Only applies when norm_method is bilinear or combined. Advanced.

  Exemple d'appel

  {"name": "analyze_melt_curves", "arguments": {"melt_table": "texte"}}

  Exemple de retour

  {"content": [{"type": "text", "text": "…"}], "structuredContent": {"count": 1, "engine": "texte", "meanTm": 1, "noPeak": 1, "reactions": "texte", "classified": "texte", "replicateSpread": "texte"}}

• annotate_region≈ 986 tokens

  Say what a genomic region holds in the reference tracks: the genes and RefSeq transcripts it overlaps, which complete coding sequences it CONTAINS (the only case where a residue-level design is honest), the DGV structural variants seen there in control populations with their frequencies, and how much of it lies in segmental duplications and how similar the best paralogue is. Every track answers with its authority, table and retrieval date. Coordinates are 1-based and inclusive, as a person writes chr17:41196312-41277500.

  Paramètres, retour & exemple (8)

  Paramètres

  • end · number · requis
    last base of the region, 1-based and inclusive.
  • build · string · requis
    the assembly the coordinates are on, by the UCSC name the cached tracks use (hg19, hg38). A build with no cached track is refused by name rather than answered empty.
  • start · number · requis
    first base of the region, 1-based.
  • _files · array · optionnel
    The project: record references shaped like _subject. Their records become library documents a tool names in sequences/parts/document; a trace or alignment is found by file name.
  • dosage · string · optionnel · any | loss | gain
    which DGV evidence is comparable: `loss` for a deletion call, `gain` for a duplication, `any` for either. Balanced and unclassified variant types (insertions, inversions) are never counted as dosage evidence, and the count of them is reported instead. Values: any (Either direction), loss (Loss), gain (Gain).
  • tracks · string · optionnel
    which tracks to read, comma-separated: `genes`, `dgv`, `segdups`. Unset reads all three. The coding verdict comes with `genes`.
  • _subject · object · optionnel
    The record to act on: exactly one of sequence, accession (+source), sample (an id from list_samples) or file ({name, text} or {name, base64}); record_index picks one record of several.
  • chromosome · string · requis
    UCSC-style sequence name; a bare `17` or `X` is read as `chr17`/`chrX`.

  Exemple d'appel

  {"name": "annotate_region", "arguments": {"end": 1, "build": "texte", "start": 1, "chromosome": "texte"}}

  Exemple de retour

  {"content": [{"type": "text", "text": "…"}], "structuredContent": {"dgv": "texte", "genes": "texte", "coding": "texte", "segdups": "texte", "summary": "texte"}}

• antibody_antigen_contacts≈ 894 tokens

  Type the ANTIBODY-ANTIGEN INTERFACE of a deposited complex: which residue of each antibody chain touches which residue of the antigen, how close, and what kind of interaction each pair makes - ionic, polar, weak polar, hydrophobic, aromatic, carbonyl, or a disulfide. The antigen is found rather than named: a protein chain with no immunoglobulin variable domain is the thing being bound. Geometric definitions are CREDO's as Arpeggio implements them, graded contact-for-contact against pdbe-arpeggio. `polar` is the hydrogen-bond criterion WITHOUT the donor angle, because a crystal structure carries no hydrogens; it is the superset an angle test would filter, and no angle-checked hydrogen bond is claimed.

  Paramètres, retour & exemple (7)

  Paramètres

  • text · string · requis
    the coordinate file's contents - a PDB flat file or a PDBx/mmCIF; the format is read from the bytes, not from a name.
  • model · number · optionnel
    which model of an ensemble to type, 1-based: conformers touch in different places, so one is typed rather than all.
  • _files · array · optionnel
    The project: record references shaped like _subject. Their records become library documents a tool names in sequences/parts/document; a trace or alignment is found by file name.
  • _subject · object · optionnel
    The record to act on: exactly one of sequence, accession (+source), sample (an id from list_samples) or file ({name, text} or {name, base64}); record_index picks one record of several.
  • antibodyChain · string · optionnel
    type only this chain against the antigen. Left out, every chain carrying a variable domain is typed.
  • antigenChains · string · optionnel
    comma-separated chain ids to treat as the antigen. Left out, every protein chain with no variable domain is the antigen.
  • interactingCutoff · number · optionnel
    atom pairs further apart than this (Å) are not reported at all; Arpeggio's own default is 5.

  Exemple d'appel

  {"name": "antibody_antigen_contacts", "arguments": {"text": "texte"}}

  Exemple de retour

  {"content": [{"type": "text", "text": "…"}], "structuredContent": {"byType": "texte", "contacts": "texte", "residues": "texte", "antigenChains": "texte", "antibodyChains": "texte"}}

• antibody_canonical_classes≈ 782 tokens

  Assign each CDR of an antibody heavy, kappa or lambda variable domain to its canonical structure class: SCALOP's length-independent clusters of known loop conformations (CDR-H1, H2, L1, L2, L3; H3 has no canonical classes). Each loop is scored against every cluster of its length by the cluster's position-specific log-odds; the best score above SCALOP's threshold names the class and its median structure (a PDB chain). Graded against the real SCALOP on every heavy, kappa and lambda chain of ANARCI's PDB benchmark.

  Paramètres, retour & exemple (6)

  Paramètres

  • _files · array · optionnel
    The project: record references shaped like _subject. Their records become library documents a tool names in sequences/parts/document; a trace or alignment is found by file name.
  • scheme · string · optionnel · imgt | chothia
    the numbering the clusters are read in. Values: imgt (IMGT), chothia (Chothia).
  • protein · string · requis
    the protein sequence (one-letter amino acids); every heavy, kappa and lambda variable domain in it is classified.
  • species · array · optionnel
    species whose HMMs are preferred when numbering (ANARCI's default: human and mouse).
  • _subject · object · optionnel
    The record to act on: exactly one of sequence, accession (+source), sample (an id from list_samples) or file ({name, text} or {name, base64}); record_index picks one record of several.
  • definition · string · optionnel · imgt | chothia | north
    where each CDR begins and ends, by SCALOP's own tables. Values: imgt (IMGT), chothia (Chothia), north (North).

  Exemple d'appel

  {"name": "antibody_canonical_classes", "arguments": {"protein": "texte"}}

  Exemple de retour

  {"content": [{"type": "text", "text": "…"}], "structuredContent": {"classes": "texte", "domains": "texte"}}

• antibody_isotype≈ 716 tokens

  Name the CONSTANT region of an antibody chain: which immunoglobulin gene and allele it carries (IGHG1, IGHA2, IGKC, IGLC2 …), and where each IMGT domain sits on it — CH1, the hinge, CH2, CH3, the secretory tail and the membrane exons, or the single C region of a light chain. A domain search says 'a C1-set immunoglobulin domain'; this says which isotype it is. Reads IMGT/GENE-DB's own per-label translations for every species, and is graded against UniProtKB's curated human constant chains and their CH1/hinge/CH2/CH3 regions.

  Paramètres, retour & exemple (5)

  Paramètres

  • _files · array · optionnel
    The project: record references shaped like _subject. Their records become library documents a tool names in sequences/parts/document; a trace or alignment is found by file name.
  • protein · string · requis
    the chain (one-letter amino acids); the constant region in it is found, so a whole heavy chain is fine.
  • species · string · optionnel
    only consider genes of this species, spelled as IMGT spells it (Homo sapiens, Mus musculus). Left out, every species in the catalogue competes and the answer says which won.
  • _subject · object · optionnel
    The record to act on: exactly one of sequence, accession (+source), sample (an id from list_samples) or file ({name, text} or {name, base64}); record_index picks one record of several.
  • minIdentity · number · optionnel
    a domain matching less of its reference than this is not reported.

  Exemple d'appel

  {"name": "antibody_isotype", "arguments": {"protein": "texte"}}

  Exemple de retour

  {"content": [{"type": "text", "text": "…"}], "structuredContent": {"gene": "texte", "allele": "texte", "domains": "texte", "species": "texte", "identity": 1}}

• antibody_liabilities≈ 608 tokens

  Scan antibody and TCR variable domains for sequence liabilities (Asn deamidation, Asp isomerization, N-glycosylation sequons, Asp-Pro cleavage, Met and Trp oxidation, unpaired or missing conserved cysteines), each placed in its IMGT region so CDR hits can be told from framework ones. Every motif is cited to its source.

  Paramètres, retour & exemple (5)

  Paramètres

  • rules · array · optionnel
    which liabilities to report (default: all).
  • _files · array · optionnel
    The project: record references shaped like _subject. Their records become library documents a tool names in sequences/parts/document; a trace or alignment is found by file name.
  • cdrOnly · boolean · optionnel
    report only liabilities that start inside a CDR.
  • protein · string · requis
    the protein sequence (one-letter amino acids).
  • _subject · object · optionnel
    The record to act on: exactly one of sequence, accession (+source), sample (an id from list_samples) or file ({name, text} or {name, base64}); record_index picks one record of several.

  Exemple d'appel

  {"name": "antibody_liabilities", "arguments": {"protein": "texte"}}

  Exemple de retour

  {"content": [{"type": "text", "text": "…"}], "structuredContent": {"count": 1, "cdrCount": 1, "liabilities": "texte"}}

• antibody_molecule≈ 719 tokens

  Properties of an assembled antibody from its heavy and light chains: molecular weight, isoelectric point, net charge at a pH, and the extinction coefficient and A280 with cysteines reduced and with every pair formed into a cystine, for a Fab (1 heavy + 1 light) or an IgG (2 + 2). Each chain keeps its own termini, so this is not the same as pasting the chains end to end. Graded against Biopython ProtParam over every heavy/light pair of ANARCI's PDB benchmark.

  Paramètres, retour & exemple (6)

  Paramètres

  • pH · number · optionnel
    the pH the net charge is reported at.
  • heavy · string · requis
    the heavy chain (one-letter amino acids), as much of it as the molecule carries.
  • light · string · requis
    the light chain (kappa or lambda, one-letter amino acids).
  • _files · array · optionnel
    The project: record references shaped like _subject. Their records become library documents a tool names in sequences/parts/document; a trace or alignment is found by file name.
  • format · string · optionnel · fab | igg
    how many copies of each chain the molecule holds. Values: fab (Fab (1 heavy + 1 light)), igg (IgG (2 heavy + 2 light)).
  • _subject · object · optionnel
    The record to act on: exactly one of sequence, accession (+source), sample (an id from list_samples) or file ({name, text} or {name, base64}); record_index picks one record of several.

  Exemple d'appel

  {"name": "antibody_molecule", "arguments": {"heavy": "texte", "light": "texte"}}

  Exemple de retour

  {"content": [{"type": "text", "text": "…"}], "structuredContent": {"absorbance": "texte", "chargeAtPH": 1, "extinction": "texte", "molecularWeight": 1, "isoelectricPoint": 1}}

• antibody_position_frequencies≈ 849 tokens

  How common each residue of an antibody variable domain is at its IMGT position, and which residues are rarer there than a cut (abYsis's 1% "unusual residue" by default). Two distributions: IMGT's own germline V and J alleles of a species (one count per reference allele), or a bundled Observed Antibody Space repertoire subset (one count per unique expressed sequence; human naive B cells, Jaffe et al. 2022). Graded against independent pandas counts of ANARCI's germline alignments and of every OAS data unit of the subset.

  Paramètres, retour & exemple (7)

  Paramètres

  • _files · array · optionnel
    The project: record references shaped like _subject. Their records become library documents a tool names in sequences/parts/document; a trace or alignment is found by file name.
  • protein · string · requis
    the protein sequence (one-letter amino acids); every antibody and T-cell-receptor variable domain in it is read.
  • species · array · optionnel
    species whose HMMs are preferred when numbering (ANARCI's default: human and mouse).
  • _subject · object · optionnel
    The record to act on: exactly one of sequence, accession (+source), sample (an id from list_samples) or file ({name, text} or {name, base64}); record_index picks one record of several.
  • rare_below · number · optionnel
    a residue is rare where its share of the alleles or sequences is below this fraction (abYsis's unusual-residue cut is 0.01).
  • distribution · string · optionnel · germline | repertoire
    what each position is counted over: `germline` (IMGT's V and J alleles of `germline_species`) or `repertoire` (the bundled human OAS subset of expressed sequences).
  • germline_species · string · optionnel
    the species whose IMGT germline alleles each position is counted over (germline distribution only; the repertoire is human).

  Exemple d'appel

  {"name": "antibody_position_frequencies", "arguments": {"protein": "texte"}}

  Exemple de retour

  {"content": [{"type": "text", "text": "…"}], "structuredContent": {"rare": "texte", "domains": "texte"}}

• apply_feature_file≈ 905 tokens

  Put the features from a GTF in this project onto the open record. A GTF lists features and their positions and carries no sequence, so this is how one reaches a molecule. It REFUSES unless something says the two are in the same coordinate space: if the file names a genome build and the record names the same one it proceeds; if they name different ones it refuses outright; if either is silent it refuses until you pass coordinates_only, which states that you are applying the intervals as positions in this record's own numbering with no genome correspondence checked. Reports what would not fit rather than trimming it.

  Paramètres, retour & exemple (5)

  Paramètres

  • file · string · optionnel
    the annotation file in this project, by name. Unset with exactly one present uses it; with several, this refuses and names them rather than picking.
  • _files · array · optionnel
    The project: record references shaped like _subject. Their records become library documents a tool names in sequences/parts/document; a trace or alignment is found by file name.
  • _subject · object · optionnel
    The record to act on: exactly one of sequence, accession (+source), sample (an id from list_samples) or file ({name, text} or {name, base64}); record_index picks one record of several.
  • sequence · string · optionnel
    the seqid within the file whose features to apply (a GTF names one per row). Unset with exactly one present uses it; with several, this refuses and names them — applying the wrong chromosome's intervals is the mistake this parameter exists to prevent.
  • coordinates_only · boolean · optionnel
    state that you are applying the intervals as COORDINATES — positions in this record’s own numbering — with no genome correspondence checked. Applying coordinates on that basis is a claim about your own data, and the run records it as the basis it used. Required whenever either side is silent about its assembly; it cannot rescue two assemblies that disagree.

  Exemple d'appel

  {"name": "apply_feature_file", "arguments": {"file": "texte", "_files": [], "_subject": {}, "sequence": "texte", "coordinates_only": true}}

  Exemple de retour

  {"content": [{"type": "text", "text": "…"}], "structuredContent": {"added": 1, "basis": "texte", "record": {}, "duplicate": 1, "outOfRange": "texte"}}

• apply_variant_call≈ 962 tokens

  Substitute one called ALT allele into a sequence and return the edited bases, the range the edit occupies and the length change. The REF allele is checked against the sequence first and a mismatch REFUSES naming both: applying a call from a different assembly would produce a construct that looks fine and is wrong. Symbolic and breakend alleles are refused for what they are: they name a rearrangement rather than replacement bases.

  Paramètres, retour & exemple (8)

  Paramètres

  • pos · number · requis
    the POS of the record to apply, 1-based as VCF writes it.
  • file · string · optionnel
    which call set the variant comes from, by name. Unset, it is the project's only one.
  • _files · array · optionnel
    The project: record references shaped like _subject. Their records become library documents a tool names in sequences/parts/document; a trace or alignment is found by file name.
  • contig · string · requis
    the contig of the record to apply, as the file names it.
  • offset · number · optionnel
    the coordinate this sequence's FIRST base has in the call set's contig. Default 1, meaning the sequence starts at the contig's start. A plasmid extracted from a genome sets this to where it was cut from, which is what lets a genomic call be applied to it at all.
  • _subject · object · optionnel
    The record to act on: exactly one of sequence, accession (+source), sample (an id from list_samples) or file ({name, text} or {name, base64}); record_index picks one record of several.
  • sequence · string · requis
    the sequence to edit.
  • alt_index · number · optionnel
    which ALT of a multiallelic record to apply, counting from 1 as the file lists them. Default the first.

  Exemple d'appel

  {"name": "apply_variant_call", "arguments": {"pos": 1, "contig": "texte", "sequence": "texte"}}

  Exemple de retour

  {"content": [{"type": "text", "text": "…"}], "structuredContent": {"delta": 1, "applied": "texte", "summary": "texte", "sequence": "texte", "edited_end": 1, "edited_start": 1}}

• assemble_index_oligos≈ 866 tokens

  Turn index sequences into the oligos a synthesiser makes: each index spliced between 5'/3' adapter arms, or onto a PCR primer in either orientation with an optional spacer. Audited for the problems that only exist once tag and oligo are concatenated and that no check of the index alone can see — a homopolymer run across the junction, a 5' tetramer recurring as its reverse complement, and an oligo over the synthesis length guideline.

  Paramètres, retour & exemple (9)

  Paramètres

  • _files · array · optionnel
    The project: record references shaped like _subject. Their records become library documents a tool names in sequences/parts/document; a trace or alignment is found by file name.
  • format · string · optionnel · adapter | primer
    adapter arms around the index, or a tagged PCR primer. Values: adapter (5'/3' adapter arms), primer (Tagged PCR primer).
  • primer · string · optionnel
    the PCR primer the tag is appended to — required when `format` is `primer`.
  • spacer · string · optionnel
    bases between the tag and the primer. Heterogeneity/phasing spacers are routine on a low-diversity library. Advanced.
  • _subject · object · optionnel
    The record to act on: exactly one of sequence, accession (+source), sample (an id from list_samples) or file ({name, text} or {name, base64}); record_index picks one record of several.
  • barcodes · array · requis
    the index sequences to assemble.
  • adapter_3 · string · optionnel
    3' arm the index is spliced before — the TruSeq read-1 primer, and the panel's own default.
  • adapter_5 · string · optionnel
    5' arm the index is spliced after — the Illumina P5, and the panel's own default.
  • reverse_complement_tag · boolean · optionnel
    append the tag as its reverse complement, as the instrument requires for some read orientations. Advanced.

  Exemple d'appel

  {"name": "assemble_index_oligos", "arguments": {"barcodes": []}}

  Exemple de retour

  {"content": [{"type": "text", "text": "…"}], "structuredContent": {"count": 1, "oligos": "texte", "longest": 1, "warnings": "texte"}}

• assemble_operon≈ 861 tokens

  Stack several CDSs into one contiguous operon, designing a fresh ribosome-binding site in front of each one AGAINST ITS REAL UPSTREAM CONTEXT — which is why the RBS for gene 2 is not the RBS design_rbs would give it in isolation. Returns the assembled sequence, its layout, and each gene's achieved strength.

  Paramètres, retour & exemple (9)

  Paramètres

  • cds · array · requis
    the coding sequences to stack, in order — wire upstream `record` outputs here, or name library documents.
  • _files · array · optionnel
    The project: record references shaped like _subject. Their records become library documents a tool names in sequences/parts/document; a trace or alignment is found by file name.
  • leader · string · optionnel
    leader placed before the FIRST ribosome-binding site (defaults to the design leader). Advanced.
  • _subject · object · optionnel
    The record to act on: exactly one of sequence, accession (+source), sample (an id from list_samples) or file ({name, text} or {name, base64}); record_index picks one record of several.
  • promoter · string · optionnel
    promoter sequence to place in front of the operon (optional). Advanced.
  • terminator · string · optionnel
    terminator sequence to place after the last gene (optional). Advanced.
  • include_subject · boolean · optionnel
    put the node's subject first, as the first gene.
  • target_strength · number · optionnel
    relative initiation strength to aim for at every gene, on the model's own scale — 1 is as strong as its reference site. Overridden per gene by `target_strengths`.
  • target_strengths · array · optionnel
    per-gene target strengths, aligned to `cds` — the Operon panel gives every row its own, and a run through this door could not say the same thing. Shorter than `cds` falls back to `target_strength` for the rest. Advanced.

  Exemple d'appel

  {"name": "assemble_operon", "arguments": {"cds": []}}

  Exemple de retour

  {"content": [{"type": "text", "text": "…"}], "structuredContent": {"genes": "texte", "layout": "texte", "record": {}, "onTarget": true, "sequence": "texte"}}

• assembly_plan_simulate≈ 828 tokens

  Run a MULTI-LEVEL assembly plan (DnaCauldron `AssemblyPlan`): several assemblies arranged into dependency levels, where each level's products become parts for the next. Emits the FINAL construct as a record. The plan is DnaCauldron's own spreadsheet shape — one row per construct, `construct_name, part, part, …`.

  Paramètres, retour & exemple (6)

  Paramètres

  • plan · string · requis
    the plan, in DnaCauldron's spreadsheet shape: one line per construct, `name,partA,partB`. A construct name may itself be used as a part in a later line — that is what makes the plan multi-level.
  • parts · array · optionnel
    the physical parts — wire upstream `record` outputs here, or list library document names/ids. A part is addressed by this NAME in the plan rows.
  • _files · array · optionnel
    The project: record references shaped like _subject. Their records become library documents a tool names in sequences/parts/document; a trace or alignment is found by file name.
  • method · string · optionnel · type2s | gibson | biobrick | basic | lcr | annealing
    the assembly chemistry every step uses (upstream passes one class per spreadsheet). Values: type2s (Golden Gate (Type-IIS)), gibson (Gibson / homologous), biobrick (BioBrick standard), basic (BASIC (linker-based)), lcr (Ligase cycling reaction), annealing (Oligo pair annealing).
  • _subject · object · optionnel
    The record to act on: exactly one of sequence, accession (+source), sample (an id from list_samples) or file ({name, text} or {name, base64}); record_index picks one record of several.
  • include_subject · boolean · optionnel
    also offer the node's subject as a part.

  Exemple d'appel

  {"name": "assembly_plan_simulate", "arguments": {"plan": "texte"}}

  Exemple de retour

  {"content": [{"type": "text", "text": "…"}], "structuredContent": {"built": 1, "failed": 1, "levels": "texte", "record": {}, "cancelled": 1, "leafParts": "texte", "constructs": "texte"}}

• assess_small_molecule≈ 1984 tokens

  Assess a small molecule given as SMILES or a molfile: RDKit's descriptors, medchem's drug-likeness rules (Lipinski, Veber, Ghose, Egan, REOS, rule of three, CNS and more) and the papers' own readings where medchem departs from them, with every bound and this molecule's value, a structural-alert screen (PAINS, Brenk, NIH, ZINC and ChEMBL's seven curated sets) with the matched atoms, the molecular formula with its masses and natural-abundance isotope pattern, QED drug-likeness under all three weightings, ESOL aqueous solubility, synthetic accessibility and natural-product likeness, the Bemis–Murcko scaffold and generic framework, the BOILED-Egg's gut-absorption and brain-penetration verdicts, and per-atom logP, polar-surface and charge contributions. Readings are taken with hydrogens implicit, the form the descriptors and the rules' papers assume. An alert flags a nuisance or reactive substructure; it is not a verdict on activity or toxicity.

  Paramètres, retour & exemple (5)

  Paramètres

  • rules · array · optionnel
    which drug-likeness rules to evaluate, by id: medchem's 17, plus the papers' own readings of Lipinski, Ghose and REOS (ids ending _paper). Every rule by default.
  • _files · array · optionnel
    The project: record references shaped like _subject. Their records become library documents a tool names in sequences/parts/document; a trace or alignment is found by file name.
  • _subject · object · optionnel
    The record to act on: exactly one of sequence, accession (+source), sample (an id from list_samples) or file ({name, text} or {name, base64}); record_index picks one record of several.
  • molecule · string · requis
    the structure: a SMILES string or an MDL molfile (V2000 or V3000). One molecule; for an SDF, pass one record.
  • alert_sets · array · optionnel
    which structural-alert catalogs to screen against. Empty screens nothing, which is not a clean result.

  Exemple d'appel

  {"name": "assess_small_molecule", "arguments": {"molecule": "texte"}}

  Exemple de retour

  {"content": [{"type": "text", "text": "…"}], "structuredContent": {"qed": "texte", "rules": "texte", "alerts": "texte", "formula": "texte", "summary": "texte", "scaffold": "texte", "boiled_egg": "texte", "solubility": "texte", "descriptors": "texte", "np_likeness": "texte", "canonical_smiles": "texte", "atom_contributions": "texte"}}

• audit_barcodes≈ 857 tokens

  Check an index set you ALREADY have, rather than designing a new one: the minimum distance between any two, how many errors that guarantees correcting, the full distance matrices, and — optionally — the subset that survives pruning to a stricter error budget. This is the question asked of a set inherited from a kit or a previous experiment.

  Paramètres, retour & exemple (6)

  Paramètres

  • _files · array · optionnel
    The project: record references shaped like _subject. Their records become library documents a tool names in sequences/parts/document; a trace or alignment is found by file name.
  • metric · string · optionnel · hamming | seqlev | levenshtein
    error model to audit against — a set safe under substitutions may be unsafe under indels. Values: hamming (Hamming (substitutions)), seqlev (Sequence-Levenshtein (indels)), levenshtein (Levenshtein).
  • _subject · object · optionnel
    The record to act on: exactly one of sequence, accession (+source), sample (an id from list_samples) or file ({name, text} or {name, base64}); record_index picks one record of several.
  • barcodes · array · requis
    the index sequences to audit.
  • prune_to_errors · number · optionnel
    also report the subset that would survive pruning to a free code correcting this many errors. 0 = do not prune. Advanced.
  • required_distance · number · optionnel
    the minimum distance the set is supposed to have — the audit says whether it does.

  Exemple d'appel

  {"name": "audit_barcodes", "arguments": {"barcodes": []}}

  Exemple de retour

  {"content": [{"type": "text", "text": "…"}], "structuredContent": {"kept": "texte", "audit": "texte", "dropped": 1, "analysis": "texte", "matrices": "texte", "distanceMap": {}}}

• audit_cds_annotations≈ 644 tokens

  Check every annotated CDS of one or more GenBank maps against its own bases and genetic code: a frame that does not close (frameshift), a stop inside the reading frame, a first codon the code cannot start with, a last codon that is not a stop, and a /translation the bases do not give. A partial end (< or >) is not judged, and a /pseudo CDS carries no flag. Where an annotation ends without a stop it reads on in frame (round the origin of a circular map) to the first stop and says how many codons that adds, whether it runs into another annotated CDS (a fusion annotated in pieces) and the read-through a random backbone of the same composition would give. Extraction and translation match Biopython on all 1,871 CDS of 695 NCBI vector records.

  Paramètres, retour & exemple (3)

  Paramètres

  • _files · array · optionnel
    The project: record references shaped like _subject. Their records become library documents a tool names in sequences/parts/document; a trace or alignment is found by file name.
  • genbank · array · requis
    the GenBank files' contents, one string per file (a file may hold several records).
  • _subject · object · optionnel
    The record to act on: exactly one of sequence, accession (+source), sample (an id from list_samples) or file ({name, text} or {name, base64}); record_index picks one record of several.

  Exemple d'appel

  {"name": "audit_cds_annotations", "arguments": {"genbank": []}}

  Exemple de retour

  {"content": [{"type": "text", "text": "…"}], "structuredContent": {"flags": "texte", "result": "texte", "flagged": "texte", "readThrough": "texte"}}

• auto_annotate≈ 1298 tokens

  Find and name known features on the subject — vector parts, origins, resistance markers and tags — by exact match, by local alignment (which finds a diverged copy and reports the identity and coverage that earned it), or by both, on either strand and across the origin, plus Cre/loxP and Gateway att recognition sites. Emits an annotated record, so a downstream map or export carries the annotations.

  Paramètres, retour & exemple (16)

  Paramètres

  • mode · string · optionnel · exact | alignment | both
    how to match a library entry: "exact" finds only a sequence spelled byte for byte, "alignment" finds a diverged copy and reports its identity and coverage, "both" runs each and keeps what only the other found.
  • lox_p · boolean · optionnel
    detect Cre/loxP-family recognition sites.
  • _files · array · optionnel
    The project: record references shaped like _subject. Their records become library documents a tool names in sequences/parts/document; a trace or alignment is found by file name.
  • policy · string · optionnel · merge | overwrite | clear
    what the emitted record does with the features it already had: `merge` keeps them all and skips a hit already there to the base, `overwrite` replaces a same-strand feature a hit overlaps, `clear` drops every existing feature first.
  • gateway · boolean · optionnel
    detect Gateway att recombination sites.
  • _subject · object · optionnel
    The record to act on: exactly one of sequence, accession (+source), sample (an id from list_samples) or file ({name, text} or {name, base64}); record_index picks one record of several.
  • libraries · array · optionnel
    which feature corpora to search, by id (an id from annotation-library/manifest.json, or "legacy" for the unsourced set). Empty means all of them.
  • max_expect · number · optionnel
    protein corpora only: the E-value a translated (six-frame) match must beat to be reported. It also sets the score the search runs at, so a stricter cutoff is a faster scan. Advanced.
  • alternatives · number · optionnel
    protein corpora only: how many runners-up to keep on each call, so a near relative is reported rather than implied. Advanced.
  • genetic_code · number · optionnel
    protein corpora only: the NCBI translation table the six frames are read under. 1 is the standard code. Advanced.
  • min_coverage · number · optionnel
    protein corpora only: drop a translated call covering less than this much of the database protein's own length. Advanced.
  • min_identity · number · optionnel
    protein corpora only: drop a translated call under this percent identity over the residues aligned. Advanced.
  • accepted_only · boolean · optionnel
    keep only hits clearing the corpus authority's own acceptance policy (>=95% identity, with a coverage bar that depends on the feature's length). Also decides overlaps: a hit the authority would reject cannot displace one it would accept. Only applies when mode is alignment or both. Advanced.
  • greedy_gateway · boolean · optionnel
    permissive att core matching — finds more sites, including partial ones. Only applies when gateway is true. Advanced.
  • hide_fragments · boolean · optionnel
    hide hits covering under 95% of their database entry, which upstream calls fragments. Only applies when mode is alignment or both. Advanced.
  • min_pi_per_match · number · optionnel
    lowest identity-weighted coverage worth reporting; upstream's own floor is 3, below which a hit is a fragment of a composite feature rather than the feature. Only applies when mode is alignment or both. Advanced.

  Exemple d'appel

  {"name": "auto_annotate", "arguments": {"mode": "exact", "lox_p": true, "_files": [], "policy": "merge", "gateway": true, "_subject": {}}}

  Exemple de retour

  {"content": [{"type": "text", "text": "…"}], "structuredContent": {"record": {}, "features": "texte", "perSource": "texte", "featureCount": 1}}

• back_translate≈ 1278 tokens

  Protein → DNA: the coding sequence that would encode a protein, weighted by a real codon-usage table. Four rules — the host's most-frequent codon (EMBOSS backtranseq), a draw from the family's real frequency distribution, the IUPAC-degenerate consensus for primers/probes (EMBOSS backtranambig), or DnaChisel's table-free first codon. It does NOT optimize: for restriction-site avoidance, a GC target or repeat removal, follow it with optimize_sequence.

  Paramètres, retour & exemple (8)

  Paramètres

  • host · string · optionnel · E. coli K-12 | H. sapiens | S. cerevisiae
    codon-usage table to weight by, named as the workbench knows it. Required for the two table-driven strategies and ignored by the other two. Tables loaded in the Back-translate or Optimizer panel this session are valid names as well as the bundled ones. Only applies when strategy is mostFrequent or weightedRandom.
  • seed · number · optionnel
    seed for the usage-weighted draw, which makes a sampled design reproducible. Omit for an unseeded draw; ignored by the three deterministic rules. Only applies when strategy is weightedRandom.
  • table · string · optionnel · Standard | Bacterial | Vertebrate Mitochondrial
    genetic code the codons are chosen under.
  • _files · array · optionnel
    The project: record references shaped like _subject. Their records become library documents a tool names in sequences/parts/document; a trace or alignment is found by file name.
  • protein · string · requis
    the protein sequence, one-letter codes (B/Z/J/U/O/X and gaps are handled and reported); wire it from translate_sequence.
  • _subject · object · optionnel
    The record to act on: exactly one of sequence, accession (+source), sample (an id from list_samples) or file ({name, text} or {name, base64}); record_index picks one record of several.
  • strategy · string · optionnel · mostFrequent | weightedRandom | ambiguous | firstCodon
    mostFrequent — EMBOSS backtranseq, and SnapGene's “Preferred Codons”: every residue takes its host's single most-used codon. | weightedRandom — Each residue is drawn from its family's real frequency distribution: a natural-looking gene rather than a run of one codon. | ambiguous — EMBOSS backtranambig: one ambiguity-coded codon covering EVERY codon for the residue. The degenerate-primer answer; needs no usage table. | firstCodon — DnaChisel's reverse_translate. Deterministic and table-free, but it is not a biological preference: use it only to reproduce a DnaChisel result.
  • append_stop · boolean · optionnel
    append a stop codon, chosen by the same strategy and table as every other codon. Skipped when the residues already end in *.

  Exemple d'appel

  {"name": "back_translate", "arguments": {"protein": "texte"}}

  Exemple de retour

  {"content": [{"type": "text", "text": "…"}], "structuredContent": {"gc": 1, "dna": "texte", "cautions": "texte", "residues": "texte", "conclusion": "texte", "provenance": "texte", "undefinedResidues": "texte", "unweightedResidues": "texte"}}

• bayesian_protein_inference≈ 1161 tokens

  Bayesian protein inference, Epifany (validated against OpenMS BayesianProteinInferenceAlgorithm on PXD000001): the posterior probability that each protein, each indistinguishable group and each peptide-spectrum match is present, from the matches' posterior error probabilities under a network in which present proteins emit their peptides. Shared peptides are weighed between their proteins instead of being counted for each.

  Paramètres, retour & exemple (15)

  Paramètres

  • beta · number · optionnel
    spurious emission probability β: the chance a peptide is reported with none of its proteins present.
  • psms · string · requis
    the matches as a table with a header row naming spectrum, peptide, charge and a posterior error probability column (tab- or comma-separated); peptides are ProForma.
  • alpha · number · optionnel
    peptide emission probability α: the chance a present protein yields a given one of its peptides.
  • gamma · number · optionnel
    protein prior γ: the chance a protein is present before any evidence.
  • _files · array · optionnel
    The project: record references shaped like _subject. Their records become library documents a tool names in sequences/parts/document; a trace or alignment is found by file name.
  • _subject · object · optionnel
    The record to act on: exactly one of sequence, accession (+source), sample (an id from list_samples) or file ({name, text} or {name, base64}); record_index picks one record of several.
  • database · string · requis
    the protein database searched, as FASTA; the accession is the header up to the first space.
  • psmCutoff · number · optionnel
    drop matches whose probability (1 − PEP) is below this.
  • gridSearch · boolean · optionnel
    choose α, β and γ instead: run OpenMS's grid (α 0.1–0.8 × β 0.01–0.4 × γ 0.2–0.7) and keep the combination whose protein posteriors best agree with target-decoy FDR and separate targets from decoys; needs decoy proteins.
  • decoyPrefix · string · optionnel
    accession prefix marking a decoy protein, for the grid search.
  • scoreColumn · string · optionnel
    the column holding each match's posterior error probability (PEP, 0 to 1).
  • ilEquivalent · boolean · optionnel
    treat isoleucine and leucine (and a database J) as the same residue when mapping peptides.
  • peptidePrior · number · optionnel
    peptide prior π, dividing each match's probability back out of its evidence.
  • appendReversedDecoys · boolean · optionnel
    add the reversed sequence of every database protein as a decoy (accession decoyPrefix + accession), for a database searched with reversed decoys that holds only targets.
  • maxAmbiguousResidues · number · optionnel
    how many ambiguous database residues (B, J, Z, X) one peptide match may resolve.

  Exemple d'appel

  {"name": "bayesian_protein_inference", "arguments": {"psms": "texte", "database": "texte"}}

  Exemple de retour

  {"content": [{"type": "text", "text": "…"}], "structuredContent": {"grid": "texte", "count": 1, "groups": "texte", "proteins": "texte", "psmPosteriors": "texte"}}

• blast_project_sequences≈ 938 tokens

  Search a sequence against THIS PROJECT'S OWN records with blastn or blastp, on this machine: the local database is built from every project record of the program's alphabet, and every E-value is computed from that database's own size. Use it to ask which of my constructs, reads or proteins carry this span. Nothing leaves the machine; for public databases use blast_search.

  Paramètres, retour & exemple (7)

  Paramètres

  • _files · array · optionnel
    The project: record references shaped like _subject. Their records become library documents a tool names in sequences/parts/document; a trace or alignment is found by file name.
  • region · string · optionnel · whole | selection | feature
    which part of the open record to search, when no sequence is wired in. Values: whole (the whole record), selection (the current selection), feature (a named feature).
  • feature · string · optionnel
    the feature's name, matched case-insensitively on the open record. Only applies when region is feature.
  • program · string · optionnel · blastn | blastp
    blastn searches the nucleotide records, blastp the protein records. Values: blastn (blastn · nucleotide query), blastp (blastp · protein query).
  • _subject · object · optionnel
    The record to act on: exactly one of sequence, accession (+source), sample (an id from list_samples) or file ({name, text} or {name, base64}); record_index picks one record of several.
  • sequence · string · optionnel
    the query. Wire a record or a sequence output, or paste raw/FASTA. Left empty, the region below is taken from the open record.
  • maxExpect · number · optionnel
    E-value cutoff (BLAST+'s -evalue); hits above it are not reported.

  Exemple d'appel

  {"name": "blast_project_sequences", "arguments": {"_files": [], "region": "whole", "feature": "texte", "program": "blastn", "_subject": {}, "sequence": "texte"}}

  Exemple de retour

  {"content": [{"type": "text", "text": "…"}], "structuredContent": {"hits": "texte", "topHit": "texte", "tabular": "texte", "hitCount": 1, "sequences": "texte", "topExpect": 1, "provenance": "texte", "topCoverage": 1, "topIdentity": 1}}

• blast_search≈ 1187 tokens

  Search a sequence against NCBI BLAST+ at EMBL-EBI (blastn, blastp, blastx, tblastn or tblastx) over ENA, UniProtKB, PDB and the vector-screening sets. This is the similarity search a methods section cites: it turns an unnamed span into named homologues with E-values, and hands the hits, the tabular report and the job id downstream. The sequence LEAVES THE MACHINE.

  Paramètres, retour & exemple (9)

  Paramètres

  • email · string · optionnel
    EBI requires a contact address on every submission (their abuse contact, not a login). Left empty, the one saved in any EMBL-EBI panel is used.
  • _files · array · optionnel
    The project: record references shaped like _subject. Their records become library documents a tool names in sequences/parts/document; a trace or alignment is found by file name.
  • region · string · optionnel · whole | selection | feature
    which part of the open record to search, when no sequence is wired in. Values: whole (the whole record), selection (the current selection), feature (a named feature).
  • feature · string · optionnel
    the feature's name, matched case-insensitively on the open record. Only applies when region is feature.
  • program · string · optionnel · blastn | blastp | blastx | tblastn | tblastx
    which BLAST program. The QUERY alphabet is derived from it and never asked for: blastx takes DNA and searches protein, tblastn the reverse. Values: blastn (blastn · dna query), blastp (blastp · protein query), blastx (blastx · dna query), tblastn (tblastn · protein query), tblastx (tblastx · dna query).
  • _subject · object · optionnel
    The record to act on: exactly one of sequence, accession (+source), sample (an id from list_samples) or file ({name, text} or {name, base64}); record_index picks one record of several.
  • sequence · string · optionnel
    the query. Wire a record or a sequence output, or paste raw/FASTA. Left empty, the region below is taken from the open record.
  • databases · array · optionnel
    database ids to search, as the service names them (em_rel, uniprotkb, pdb, emvec…). Several are searched together. Left empty, the service's OWN default for this program's context is used and reported back.
  • parameters · string · optionnel
    every other advertised parameter, one `id=value` per line, using the service's own ids (exp, matrix, filter, gapopen, gapext, wordsize, alignments, scores, taxids…). Left empty each keeps the service's default for this context. An id the service does not advertise is refused by name rather than dropped.

  Exemple d'appel

  {"name": "blast_search", "arguments": {"email": "texte", "_files": [], "region": "whole", "feature": "texte", "program": "blastn", "_subject": {}}}

  Exemple de retour

  {"content": [{"type": "text", "text": "…"}], "structuredContent": {"hits": "texte", "jobId": "texte", "topHit": "texte", "tabular": "texte", "hitCount": 1, "sequences": "texte", "topExpect": 1, "provenance": "texte", "topCoverage": 1, "topIdentity": 1}}

• bootstrap_cq≈ 1562 tokens

  Resampling error bars on ONE reaction's Cq. A Cq is read off a fitted model, so its uncertainty is how tightly the observations pin that model down - which propagating a measured spread cannot answer. This refits the curve a few hundred times, either by resampling its residuals or by leaving observations out, and reports the spread of everything the fit produces: every model coefficient, the Cq under each definition, the efficiency and the initial fluorescence, each with the quantiles of the iterations rather than a normal approximation, so an asymmetric interval means the estimate genuinely is asymmetric. Reproduces qpcR 1.4.2's `pcrboot`.

  Paramètres, retour & exemple (12)

  Paramètres

  • drop · number · optionnel
    jackknife only: observations left out of each refit. 1 is the delete-one jackknife; more is a delete-d jackknife, which is less sensitive to a single influential cycle. Only applies when scheme is jack.
  • seed · number · optionnel
    R's `set.seed` value, so the interval is reproducible and citable. Advanced.
  • model · string · optionnel · l4 | l5 | l6 | l7 | b4 | b5 | b6 | b7
    the sigmoid fitted once and REFITTED on every iteration. It is not re-chosen per resample: Cqs fitted under different models are not comparable, so a mixture over models would make the quantiles mean nothing. Values: l4 (l4 · 4-param log-logistic), l5 (l5 · + asymmetry), l6 (l6 · + linear baseline drift), l7 (l7 · + quadratic baseline), b4 (b4 · 4-param logistic (raw scale)), b5 (b5 · + asymmetry), b6 (b6 · + linear baseline drift), b7 (b7 · + quadratic baseline).
  • _files · array · optionnel
    The project: record references shaped like _subject. Their records become library documents a tool names in sequences/parts/document; a trace or alignment is found by file name.
  • curves · string · requis
    the amplification table: a header row, first column the cycle number and every other column one reaction's fluorescence. The same parser `call_cq` and the Curve->Cq tab use.
  • scheme · string · optionnel · boot | jack
    `boot` resamples the fit's residuals (upstream's default); `jack` leaves observations out. The bootstrap answers "how would this Cq move under the same noise?", the jackknife "how much does any single cycle carry it?".
  • _subject · object · optionnel
    The record to act on: exactly one of sequence, accession (+source), sample (an id from list_samples) or file ({name, text} or {name, base64}); record_index picks one record of several.
  • reaction · string · optionnel
    which reaction to resample, by its column name. Blank takes the first column — this is a per-reaction run by design, because at the default 200 iterations a 47-reaction plate would be 9,400 refits nobody asked for.
  • cq_method · string · optionnel · cpD2 | cpD1 | maxE | expR | Cy0 | CQ | maxRatio
    which Cq definition the resampled efficiency readouts report. Values: cpD2 (cpD2 · second-derivative max), cpD1 (cpD1 · first-derivative max), maxE (maxE · cycle of maximum efficiency), expR (expR · exponential region), Cy0 (Cy0 · tangent x-intercept (Guescini)), CQ (CQ · 20 % of the Cq fluorescence), maxRatio (maxRatio · spline, model-free (Shain)).
  • conf_level · number · optionnel
    the level the reported bounds are read at — 0.95 puts them at the 2.5 % and 97.5 % quantiles of the iterations.
  • iterations · number · optionnel
    each iteration is a full nonlinear refit, so this is the run's whole cost. 100 is upstream's default and puts a 95 % bound on a single order statistic, which is why both doors open on 200.
  • include_readouts · boolean · optionnel
    also resample every efficiency readout — the Cq definitions, the efficiency, the initial fluorescence — not just the model coefficients. On, because an interval on the Cq is the point; off is faster and returns coefficients alone. Advanced.

  Exemple d'appel

  {"name": "bootstrap_cq", "arguments": {"curves": "texte"}}

  Exemple de retour

  {"content": [{"type": "text", "text": "…"}], "structuredContent": {"rss": "texte", "rmse": "texte", "model": "texte", "reaction": "texte", "readouts": "texte", "confLevel": 1, "converged": 1, "iterations": 1, "coefficients": "texte"}}

• browse_region≈ 966 tokens

  Read one window of a genome the way a genome browser shows it: the cytogenetic bands it spans, the transcripts in the chosen RefSeq set, which residues of each protein the window encodes (translated from the assembly’s own bases), how many dbSNP 155 variants fall in it and how many ClinVar calls pathogenic, and every CRISPR site for the chosen nuclease (SpCas9 unless told otherwise) with its strand, cut position and on-target scores. Give a gene symbol (resolved through MANE Select, then HGNC) or a locus, 1-based and inclusive. Each lane refuses a window wider than it will read, and says so.

  Paramètres, retour & exemple (7)

  Paramètres

  • gene · string · optionnel
    a gene symbol; the window is its MANE Select (or HGNC) transcript with a 2% margin either side. Takes precedence over `locus`.
  • locus · string · optionnel
    the window, 1-based and inclusive, when no `gene` is given.
  • _files · array · optionnel
    The project: record references shaped like _subject. Their records become library documents a tool names in sequences/parts/document; a trace or alignment is found by file name.
  • _subject · object · optionnel
    The record to act on: exactly one of sequence, accession (+source), sample (an id from list_samples) or file ({name, text} or {name, base64}); record_index picks one record of several.
  • assembly · string · requis
    the UCSC assembly name (hg38, hg19, mm39…).
  • nuclease · string · optionnel · SpCas9 | SpCas9-NG | SpG | SpRY | xCas9 | SaCas9 | SaCas9-KKH | AsCas12a
    which nuclease the CRISPR sites are enumerated for (its PAM and cut rule). On-target scores are SpCas9-trained and come back null for any other. Values: SpCas9 (SpCas9 · NGG), SpCas9-NG (SpCas9-NG · NG), SpG (SpG · NGN), SpRY (SpRY · NRN), xCas9 (xCas9 · NG), SaCas9 (SaCas9 · NNGRRT), SaCas9-KKH (SaCas9-KKH · NNNRRT), AsCas12a (AsCas12a · TTTV), LbCas12a (LbCas12a · TTTV), enAsCas12a (enAsCas12a · TTTV).
  • gene_track · string · optionnel · ncbiRefSeqSelect | ncbiRefSeqCurated | ncbiRefSeq | ncbiRefSeqPredicted
    which RefSeq set the transcripts and protein residues come from. Values: ncbiRefSeqSelect (RefSeq Select and MANE), ncbiRefSeqCurated (RefSeq Curated), ncbiRefSeq (RefSeq All), ncbiRefSeqPredicted (RefSeq Predicted).

  Exemple d'appel

  {"name": "browse_region", "arguments": {"assembly": "texte"}}

  Exemple de retour

  {"content": [{"type": "text", "text": "…"}], "structuredContent": {"sites": "texte", "window": "texte", "protein": "texte", "summary": "texte", "refusals": "texte"}}

• build_addgene_deposit≈ 698 tokens

  Fill Addgene's own deposit spreadsheet from a record: one row per plasmid with its name and sequence, plus your answers for every plasmid (purpose, plasmid type, cloning method, resistance, growth strain and the other drop-downs). The sheet is fetched from Addgene each run, so its columns and choices are current; a value it would refuse is left out and named, and `columns` lists every column with its choices. It WRITES A FILE and sends nothing.

  Paramètres, retour & exemple (4)

  Paramètres

  • _files · array · optionnel
    The project: record references shaped like _subject. Their records become library documents a tool names in sequences/parts/document; a trace or alignment is found by file name.
  • answers · object · optionnel
    the sheet's columns to fill for every plasmid, header → value, e.g. {"Purpose": "Expresses EGFP in E. coli", "Bacterial Resistance": "Ampicillin"}. A drop-down column takes one of its own choices; run once without answers to read them from `columns`.
  • genbank · string · requis
    the plasmids to deposit, as GenBank text: one row per nucleotide record.
  • _subject · object · optionnel
    The record to act on: exactly one of sequence, accession (+source), sample (an id from list_samples) or file ({name, text} or {name, base64}); record_index picks one record of several.

  Exemple d'appel

  {"name": "build_addgene_deposit", "arguments": {"genbank": "texte"}}

  Exemple de retour

  {"content": [{"type": "text", "text": "…"}], "structuredContent": {"file": "texte", "columns": "texte", "reading": "texte", "written": 1, "problems": "texte"}}

• build_assembly_report≈ 952 tokens

  Build DnaCauldron's assembly report from an assembly result: the per-construct summary table, the constructs and errors spreadsheets as pandas-compatible CSV, and the Outcome / Number of assemblies stats. Wire `golden_gate_assemble` or `gibson_assemble`'s `products`, `errors` and `warnings` outputs into it.

  Paramètres, retour & exemple (7)

  Paramètres

  • _files · array · optionnel
    The project: record references shaped like _subject. Their records become library documents a tool names in sequences/parts/document; a trace or alignment is found by file name.
  • enzyme · string · optionnel
    the Type-IIS enzyme, for a method that has one — it becomes the report's `enzymes` column, mirroring DnaCauldron's `Type2sRestrictionAssembly.get_extra_construct_data()`. Leave it empty for Gibson, which has no enzyme: an empty column would imply one exists.
  • errors · array · optionnel
    structured assembly errors — wire the assembly node's `errors` output. These become the errors spreadsheet, which is the most useful thing in a report about a run that did not work.
  • _subject · object · optionnel
    The record to act on: exactly one of sequence, accession (+source), sample (an id from list_samples) or file ({name, text} or {name, base64}); record_index picks one record of several.
  • products · array · optionnel
    the enumerated constructs — wire an assembly node's `products` output. Each needs `id`, `sequence` and `fragmentNames`, which is what both assembly nodes emit.
  • warnings · array · optionnel
    structured assembly warnings — wire the assembly node's `warnings` output.
  • assembly_name · string · optionnel
    the name for this assembly: the `assembly_name` column of the summary table and the first field of every errors row.

  Exemple d'appel

  {"name": "build_assembly_report", "arguments": {"_files": [], "enzyme": "texte", "errors": [], "_subject": {}, "products": [], "warnings": []}}

  Exemple de retour

  {"content": [{"type": "text", "text": "…"}], "structuredContent": {"stats": "texte", "report": "texte", "errorsCsv": "texte", "partsUsed": "texte", "summaryCsv": "texte", "summaryText": "texte", "warningsCsv": "texte", "constructCount": 1}}

• build_ena_submission≈ 1148 tokens

  Turn a record into what ENA's Webin-CLI takes for an annotated sequence (`-context sequence`): an ENA flat file (`.embl`) and its manifest. Features are checked against the tables ENA's own validator reads, so what Webin-CLI would refuse (an unknown key, a missing mandatory qualifier, a double quote in a value, a duplicate feature) is refused or rewritten here, by name. A description under 10 characters, an entry under 100 bp and a missing study are reported first. It WRITES FILES and sends nothing.

  Paramètres, retour & exemple (10)

  Paramètres

  • study · string · optionnel
    the Webin Portal study accession (PRJEB… or ERP…). Webin-CLI refuses a set without one; left empty, the files are written and the reason reported.
  • _files · array · optionnel
    The project: record references shaped like _subject. Their records become library documents a tool names in sequences/parts/document; a trace or alignment is found by file name.
  • genbank · string · requis
    the record to submit, as GenBank text. Its features, topology and DEFINITION are read from it.
  • _subject · object · optionnel
    The record to act on: exactly one of sequence, accession (+source), sample (an id from list_samples) or file ({name, text} or {name, base64}); record_index picks one record of several.
  • mol_type · string · optionnel · genomic DNA | genomic RNA | mRNA | rRNA | tRNA | other RNA | other DNA | transcribed RNA
    the source feature's mandatory /mol_type. `other DNA` is the INSDC value for a synthetic construct.
  • organism · string · optionnel
    the scientific name of the source organism; ENA checks it against its taxonomy. `synthetic construct` is a real answer for a built vector.
  • topology · string · optionnel · | circular | linear
    circular for a plasmid (the ID line; only then may a feature cross the origin). Left empty, the record's own topology is used. Values: (From the record), circular (Circular), linear (Linear). Advanced.
  • description · string · optionnel
    the DE line, what the sequence is. Left empty, each record's own DEFINITION is used; ENA refuses one shorter than 10 characters.
  • geo_loc_name · string · optionnel
    where the sample came from, from the INSDC vocabulary, or a missing-value term.
  • collection_date · string · optionnel
    when the sample was collected, on the source feature. Optional, but must be INSDC-legal; a construct takes a missing-value term such as `missing: lab stock`.

  Exemple d'appel

  {"name": "build_ena_submission", "arguments": {"genbank": "texte"}}

  Exemple de retour

  {"content": [{"type": "text", "text": "…"}], "structuredContent": {"files": "texte", "changes": "texte", "command": "texte", "reading": "texte", "written": 1, "flatFile": "texte", "problems": "texte"}}

• build_genbank_submission≈ 1306 tokens

  Turn a record into the SUBMISSION SET NCBI's `table2asn` consumes: a `.fsa` whose defline carries the source modifiers, and a 5-column feature table (`.tbl`) beside it. This is not a GenBank export — GenBank's submission pipeline takes neither a `.gb` nor a plain fasta. Its real work is REFUSING and MIGRATING what GenBank will not accept: twelve feature keys were retired in 2014 in favour of `regulatory` (promoter, terminator and RBS among them, so every plasmid map is affected), a qualifier not on a key's approved list is dropped by name, and an unapproved key is kept as a `misc_feature` carrying its original name. Since December 2024 GenBank has required `collection_date` and `geo_loc_name` on every submission, and both are validated here against the INSDC vocabularies BEFORE a file is written. It WRITES FILES and sends nothing: no account, no key, no upload — `table2asn` stays yours to run, and the submission template it also wants is yours to make.

  Paramètres, retour & exemple (8)

  Paramètres

  • _files · array · optionnel
    The project: record references shaped like _subject. Their records become library documents a tool names in sequences/parts/document; a trace or alignment is found by file name.
  • genbank · string · requis
    the record to submit, as GenBank text. Its features and topology are read from it — wire it from an export, or paste it.
  • _subject · object · optionnel
    The record to act on: exactly one of sequence, accession (+source), sample (an id from list_samples) or file ({name, text} or {name, base64}); record_index picks one record of several.
  • mol_type · string · optionnel · genomic DNA | genomic RNA | mRNA | rRNA | tRNA | other RNA | other DNA | transcribed RNA
    one of INSDC's two MANDATORY qualifiers on the source key. Omitting it lets table2asn choose, which is a scientific fact picked by a tool.
  • organism · string · optionnel
    the scientific name of the source organism. `synthetic construct` is a real answer for a built vector, not an absence.
  • topology · string · optionnel · | circular | linear
    circular for a plasmid. With this omitted table2asn writes `linear` into the LOCUS line, so a plasmid is deposited as a linear molecule with no error anywhere. Left empty, the record's own topology is used. Values: (From the record), circular (Circular), linear (Linear). Advanced.
  • geo_loc_name · string · optionnel
    where the sample came from: a country, ocean or sea from the INSDC vocabulary, optionally `:region` and `, locality`. MANDATORY since December 2024, and it takes the same missing-value terms.
  • collection_date · string · optionnel
    when the sample was collected. MANDATORY on every GenBank submission since December 2024. `DD-Mmm-YYYY`, `Mmm-YYYY`, `YYYY`, an ISO form, or two of them separated by `/` for a range. A construct that was never collected anywhere takes an INSDC missing-value term such as `missing: lab stock`.

  Exemple d'appel

  {"name": "build_genbank_submission", "arguments": {"genbank": "texte"}}

  Exemple de retour

  {"content": [{"type": "text", "text": "…"}], "structuredContent": {"files": "texte", "changes": "texte", "command": "texte", "reading": "texte", "written": 1, "problems": "texte", "featureTable": "texte"}}

• build_tree≈ 4894 tokens

  Build a phylogeny from aligned sequences — distance methods (NJ, BIONJ, FastME, UPGMA/WPGMA), parsimony, maximum likelihood, or Bayesian MCMC under a strict clock and coalescent prior — with branch support from a bootstrap, aLRT or aBayes, or, for the Bayesian method, clade posterior probabilities. Wire it downstream of align_sequences.

  Paramètres, retour & exemple (49)

  Paramètres

  • gamma · number · optionnel
    gamma shape for among-site rate variation in the DISTANCE correction; 0 disables. Not the ML +Γ, which is `ml_gamma_categories`. Advanced.
  • model · string · optionnel · raw | N | TS | TV | JC69 | K80 | F81 | K81
    distance/substitution model (ape's names). K80 is the engine's default; very divergent sequences need raw or JC69.
  • _files · array · optionnel
    The project: record references shaped like _subject. Their records become library documents a tool names in sequences/parts/document; a trace or alignment is found by file name.
  • method · string · optionnel · nj | bionj | fastme-bal | fastme-ols | upgma | wpgma | parsimony | ml
    tree-building method; distance methods are fast, ML is the slowest and best-justified. Values: nj (Neighbor-Joining), bionj (BIONJ), fastme-bal (FastME (balanced)), fastme-ols (FastME (OLS)), upgma (UPGMA), wpgma (WPGMA), parsimony (Maximum Parsimony), ml (Maximum Likelihood), bayesian (Bayesian (MCMC)).
  • _subject · object · optionnel
    The record to act on: exactly one of sequence, accession (+source), sample (an id from list_samples) or file ({name, text} or {name, base64}); record_index picks one record of several.
  • ml_model · string · optionnel · JC69 | F81 | K80 | HKY | TN93 | GTR
    ML substitution model. Values: JC69 (JC69), F81 (F81), K80 (K80), HKY (HKY), TN93 (TN93), GTR (GTR). Only applies when method is ml, or when support_method is alrt or abayes or shalrt. Advanced.
  • ml_shape · number · optionnel
    α of the discrete-Γ distribution over site rates — lower means more rate variation between sites. The starting value when the shape is estimated, and the fixed value when it is not. Inert while `ml_gamma_categories` is 1, because one category has no spread. Only applies when method is ml, or when support_method is alrt or abayes or shalrt. Advanced.
  • bootstrap · number · optionnel
    bootstrap replicates; 0 disables. Each replicate rebuilds the whole tree, so cost scales with it — 100 is the conventional minimum for a published tree and is the panel's default. Only applies when support_method is bootstrap.
  • ladderize · boolean · optionnel
    order each node's children by clade size, so the drawing reads as a ladder. Changes the Newick's child order and nothing about the topology. Advanced.
  • sequences · array · optionnel
    aligned sequences — wire align_sequences' rows here, or name library documents.
  • fastme_nni · boolean · optionnel
    FastME refinement by nearest-neighbour interchange (ape's `nni = TRUE`). Only applies when method is fastme-bal or fastme-ols. Advanced.
  • fastme_spr · boolean · optionnel
    FastME balanced refinement by subtree prune-and-regraft (ape's `spr = TRUE`). Only applies when method is fastme-bal. Advanced.
  • ml_invariant · number · optionnel
    proportion of sites that never change; 0 disables. The starting value when it is estimated. Only applies when method is ml, or when support_method is alrt or abayes or shalrt. Advanced.
  • bayesian_runs · number · optionnel
    independent runs (MrBayes nruns), seeded seed, seed+1, ...; 2 or more pools their samples and reports the average standard deviation of split frequencies and the PSRF. Only applies when method is bayesian.
  • bayesian_seed · number · optionnel
    seed of the chain; the same seed and settings reproduce the same samples. Only applies when method is bayesian. Advanced.
  • bayesian_temp · number · optionnel
    heating increment (MrBayes temp): chain j samples the posterior raised to 1/(1 + temp*j). Only applies when method is bayesian. Advanced.
  • midpoint_root · boolean · optionnel
    root the result at its midpoint — a drawing convention, not evidence about where the true root is. Advanced.
  • sh_replicates · number · optionnel
    RELL replicates behind `shalrt` — resamples the three fits' per-site log-likelihoods, not the alignment, so a replicate costs microseconds rather than a whole re-inference. PhyML uses 10,000. Ignored unless `support_method` is `shalrt`. Only applies when support_method is shalrt. Advanced.
  • bayesian_clock · string · optionnel · strict | ucln | none
    clock model: strict (one rate on every branch), ucln, the uncorrelated lognormal relaxed clock (each branch its own rate, mean 1, log-scale sd sampled under Exponential(mean 1/3), as BEAST's UCRelaxedClockModel), or none: an unrooted tree with free branch lengths under an Exponential prior and no coalescent (MrBayes' unconstrained model). Only applies when method is bayesian.
  • bayesian_kappa · number · optionnel
    transition/transversion ratio for K80/HKY, held fixed. Only applies when method is bayesian.
  • bayesian_model · string · optionnel · JC69 | F81 | K80 | HKY
    substitution model for the Bayesian chain, its parameters held fixed for the run: base frequencies are the alignment's own for F81/HKY, and kappa is `bayesian_kappa` for K80/HKY. Values: JC69 (JC69), F81 (F81), K80 (K80), HKY (HKY). Only applies when method is bayesian.
  • bayesian_shape · number · optionnel
    Gamma shape (alpha) for +G, held fixed for the run; smaller means more rate variation among sites. Only applies when method is bayesian.
  • bootstrap_seed · number · optionnel
    seed for whichever resampling this run does — the bootstrap's replicates, or SH-aLRT's. The same seed always reproduces the same support values. Only applies when support_method is bootstrap or shalrt. Advanced.
  • support_method · string · optionnel · bootstrap | alrt | abayes | shalrt
    which branch support to attach. `bootstrap` resamples alignment columns and rebuilds the tree per replicate (uses `bootstrap`/`bootstrap_seed`). The three branch tests re-infer nothing: they score each internal branch against its two nearest-neighbour rearrangements under the ML model, three likelihood evaluations per branch instead of N whole re-inferences. `alrt` is the parametric test of Anisimova & Gascuel (2006), read against a mixture-of-chi-squares null, and it saturates at 99.985%. `abayes` is the Bayesian support of Anisimova et al. (2011). `shalrt` is the Shimodaira-Hasegawa-corrected variant (PhyML `-b -4`): the same three fits, but the gap is read against a null built by RELL-resampling their per-site log-likelihoods `sh_replicates` times from `bootstrap_seed` — slower than the other two, does not saturate, and usually more conservative. All three use `ml_model`/`ml_gamma_categories`/`ml_shape`/`ml_invariant` for the model, whichever `method` built the tree. Values: bootstrap (Bootstrap), alrt (aLRT), abayes (aBayes), shalrt (SH-aLRT).
  • bayesian_chains · number · optionnel
    Metropolis-coupled chains per run (MrBayes nchains; its default is 4): the extra chains sample a flattened posterior and swap states with the cold one, so a run can cross valleys a single chain cannot. Each chain costs a full chain's time. Only applies when method is bayesian.
  • include_subject · boolean · optionnel
    also include the node's subject.
  • bayesian_burn_in · number · optionnel
    iterations discarded from the start. Only applies when method is bayesian.
  • ml_rearrangement · string · optionnel · nni | spr | tbr
    topology search moves for the ML fit. `nni` moves one subtree past its neighbour and stops at the first topology no single move improves, which is a local optimum. `spr` runs that first and then sweeps prune-and-regraft, which reaches trees NNI cannot — at a quadratic number of rearrangements per sweep rather than a linear one. `tbr` runs both and then sweeps tree bisection and reconnection, which cuts a branch and rejoins the two halves by any pair of their branches: the largest neighbourhood here, measured at 1,950 distinct topologies against SPR's 814 on an 18-taxon tree, so roughly 2.4x an SPR sweep. Ignored unless `method` is `ml` and `ml_optimise_topology` is on. Values: nni (NNI), spr (NNI, then SPR), tbr (NNI, then SPR, then TBR). Only applies when method is ml. Advanced.
  • bayesian_clock_sd · number · optionnel
    where the relaxed clock's sigma (log-scale sd of branch rates) starts; always sampled. Only applies when bayesian_clock is ucln. Advanced.
  • bootstrap_measure · string · optionnel · fbp | tbe
    which bootstrap statistic to report. `fbp` is Felsenstein's proportion: the share of replicates that carry this exact branch: a yes/no question per replicate, so one taxon landing elsewhere makes the answer no, which is why a well-supported clade can read near zero on a large tree. `tbe` is the transfer bootstrap expectation (Lemoine et al. 2018, Nature 556:452-456): 1 minus the average number of taxa that would have to move to turn a replicate's nearest branch into this one, over the branch's depth. TBE reads higher than FBP on the same replicates and the two are NOT interchangeable, so say which one a number is. Both read the SAME replicates, so `tbe` costs no extra inference. Only applies when support_method is bootstrap.
  • ml_optimise_rates · boolean · optionnel
    fit the substitution rates rather than holding the model's own. Only applies when method is ml. Advanced.
  • ml_optimise_shape · boolean · optionnel
    fit the discrete-Γ shape rather than holding `ml_shape`. Costs a degree of freedom in AIC/BIC, and does nothing while `ml_gamma_categories` is 1. Only applies when method is ml. Advanced.
  • pairwise_deletion · boolean · optionnel
    exclude a gapped site only from the pairs it is missing in, rather than from every pair. ape's default is off (complete deletion), which keeps distances mutually comparable but discards a column if ANY sequence has a gap there — turn this on for gappy alignments.
  • bayesian_brlen_rate · number · optionnel
    with no clock: rate of the Exponential prior on each branch length (MrBayes brlenspr=unconstrained:exp(rate)); 10 means a prior mean of 0.1 substitutions per site. Only applies when bayesian_clock is none. Advanced.
  • bayesian_iterations · number · optionnel
    Metropolis-Hastings proposals. Each rescores the alignment, so time grows with iterations x taxa x site patterns. Only applies when method is bayesian.
  • ml_gamma_categories · number · optionnel
    discrete-Γ rate categories for the rate heterogeneity across sites; 1 disables it. Only applies when method is ml, or when support_method is alrt or abayes or shalrt. Advanced.
  • bayesian_theta_shape · number · optionnel
    shape of the Gamma prior on theta. Only applies when method is bayesian. Advanced.
  • bayesian_theta_start · number · optionnel
    starting theta of the chain (not a prior). Only applies when method is bayesian. Advanced.
  • ml_optimise_topology · boolean · optionnel
    let the ML search move the topology. With this off the result is the Neighbor-Joining topology with ML branch lengths, and the engine says so in a warning. Only applies when method is ml. Advanced.
  • bayesian_sample_kappa · boolean · optionnel
    sample kappa (K80/HKY) under MrBayes' Beta(1,1) prior on kappa/(1+kappa), starting from bayesian_kappa. Only applies when method is bayesian.
  • bayesian_sample_shape · boolean · optionnel
    sample the Gamma shape under MrBayes' Exponential(1) prior instead of holding it at bayesian_shape (which becomes the start); needs bayesian_gamma_categories > 1. Only applies when method is bayesian.
  • ml_optimise_invariant · boolean · optionnel
    fit the proportion of invariant sites rather than holding `ml_invariant`. Costs a degree of freedom in AIC/BIC. Only applies when method is ml. Advanced.
  • bayesian_min_part_freq · number · optionnel
    a clade enters the split-frequency deviation only if some run sampled it at least this share of the time (MrBayes minpartfreq). Only applies when method is bayesian. Advanced.
  • parsimony_rearrangement · string · optionnel · nni | spr | tbr
    parsimony topology search: `nni` hill-climbs by nearest-neighbour interchange, `spr` adds prune-and-regraft when NNI stalls (phangorn's own default), `tbr` adds bisect-and-reconnect when SPR stalls. Nested, not alternatives: each runs the cheaper moves first, because every NNI move is an SPR move and every SPR move is a TBR move. `tbr` searches the largest neighbourhood this tool offers — 1,950 distinct topologies against SPR's 814 on an 18-taxon tree — and rescores each candidate whole, where SPR scores incrementally, so it is markedly the slowest. Values: nni (Nearest-neighbour interchange), spr (Subtree prune-and-regraft), tbr (Tree bisection and reconnection). Only applies when method is parsimony. Advanced.
  • bayesian_gamma_categories · number · optionnel
    discrete-Gamma categories for among-site rate variation (+G, each category its bin mean); 1 is equal rates. Only applies when method is bayesian.
  • bayesian_sample_frequency · number · optionnel
    keep one tree every this many iterations after burn-in. Only applies when method is bayesian. Advanced.
  • bayesian_theta_prior_mean · number · optionnel
    mean of the Gamma prior on theta = 4N mu, in substitutions per site. Only applies when method is bayesian. Advanced.
  • bayesian_sample_frequencies · boolean · optionnel
    sample the base frequencies (F81/HKY) under a flat Dirichlet, starting from the alignment's own. Only applies when method is bayesian.
  • ml_optimise_base_frequencies · boolean · optionnel
    fit base frequencies rather than holding them equal. Only applies when method is ml. Advanced.

  Exemple d'appel

  {"name": "build_tree", "arguments": {"gamma": 1, "model": "raw", "_files": [], "method": "nj", "_subject": {}, "ml_model": "JC69"}}

  Exemple de retour

  {"content": [{"type": "text", "text": "…"}], "structuredContent": {"gamma": 1, "gammaP": 1, "newick": "texte", "bayesian": "texte", "tipCount": 1, "transfer": "texte", "warnings": "texte", "statistics": "texte", "distanceMap": {}, "branchSupport": "texte", "distanceMatrix": "texte", "clockDeviationInBranches": 1}}

• calculate_power≈ 2358 tokens

  Power and sample size for a planned experiment: how many replicates a test needs to detect an effect, or what power, detectable effect or significance level a design that is already fixed gives. Leave ONE quantity out with `solve_for` and it is solved; everything else is given. Thirteen tests in two families: Cohen's standardized effect sizes (pwr 1.3-0: t one/two-sample/paired and unequal n, one and two proportions by arcsine h, normal mean, correlation, chi-square w, one-way ANOVA f, linear-model f²) and raw units (R's power.t.test from a difference and SD, power.prop.test from two proportions, power.anova.test from variances). Every number is R's, reproduced: the solved value is uniroot's root at R's tolerance, and an unreachable target is refused with R's own message. Returns the power curve around the answer and the R call that reproduces it.

  Paramètres, retour & exemple (26)

  Paramètres

  • N · number · optionnel
    total observations across every cell. Only applies when test is chisq.
  • k · number · optionnel
    number of groups. Only applies when test is anova.
  • n · number · optionnel
    observations per group (pairs, for paired; the sample, for one-sample and correlation). Only applies when test is t or two_proportions or one_proportion or normal_mean or correlation or anova or t_raw or proportions_raw or anova_raw.
  • u · number · optionnel
    numerator degrees of freedom: the number of predictors tested. Only applies when test is linear_model.
  • v · number · optionnel
    denominator degrees of freedom: n − u − 1 for n observations. Only applies when test is linear_model.
  • df · number · optionnel
    degrees of freedom of the chi-square test: (cells − 1) for goodness of fit, (rows − 1)(columns − 1) for independence. Only applies when test is chisq.
  • n1 · number · optionnel
    observations in the first group. Only applies when test is t_unequal or two_proportions_unequal.
  • n2 · number · optionnel
    observations in the second group. Only applies when test is t_unequal or two_proportions_unequal.
  • p1 · number · optionnel
    the proportion in group 1. Only applies when test is proportions_raw.
  • p2 · number · optionnel
    the proportion in group 2. Only applies when test is proportions_raw.
  • sd · number · optionnel
    the standard deviation, in the same units (of the differences, for paired); R's default is 1. Only applies when test is t_raw.
  • test · string · requis · t | t_unequal | two_proportions | two_proportions_unequal | one_proportion | normal_mean | correlation | chisq
    which test the experiment will be analyzed with; the power answer belongs to that test and no other. Values: t (t test: one-sample, two-sample or paired, Cohen's d), t_unequal (two-sample t test, unequal group sizes, Cohen's d), two_proportions (two proportions, equal n, Cohen's h), two_proportions_unequal (two proportions, unequal n, Cohen's h), one_proportion (one proportion against a null value, Cohen's h), normal_mean (normal mean, known variance, effect d), correlation (Pearson correlation, r), chisq (chi-square goodness of fit or independence, Cohen's w), anova (balanced one-way ANOVA, Cohen's f), linear_model (linear model F test (multiple regression), Cohen's f²), t_raw (t test in raw units: difference and standard deviation), proportions_raw (two proportions in raw units: p1 and p2), anova_raw (balanced one-way ANOVA in raw units: between- and within-group variance).
  • type · string · optionnel · two.sample | one.sample | paired
    the t test's design. Only applies when test is t or t_raw.
  • power · number · optionnel
    1 − β, the chance of detecting the effect if it is real. No default: the target is yours to choose.
  • _files · array · optionnel
    The project: record references shaped like _subject. Their records become library documents a tool names in sequences/parts/document; a trace or alignment is found by file name.
  • effect · number · optionnel
    the standardized effect: Cohen's d for t and normal-mean tests, h for proportions, r for correlation, w for chi-square, f for ANOVA, f² for the linear model. Give a value or `effect_size` instead. Only applies when test is t or t_unequal or two_proportions or two_proportions_unequal or one_proportion or normal_mean or correlation or chisq or anova or linear_model.
  • groups · number · optionnel
    number of groups. Only applies when test is anova_raw.
  • strict · boolean · optionnel
    two-sided raw-unit tests: also count rejections in the wrong tail, as R's strict = TRUE. Only applies when test is t_raw or proportions_raw. Advanced.
  • _subject · object · optionnel
    The record to act on: exactly one of sequence, accession (+source), sample (an id from list_samples) or file ({name, text} or {name, base64}); record_index picks one record of several.
  • sig_level · number · optionnel
    α, the type I error rate; R's default.
  • solve_for · string · optionnel · n | n1 | n2 | N | k | groups | u | v
    the one quantity to solve. Left unset it is the test's sample size (n; n2 for unequal groups, N for chi-square, v for the linear model). `effect` solves the smallest detectable effect.
  • difference · number · optionnel
    δ, the true difference in means, in the measurement's units. Only applies when test is t_raw.
  • within_var · number · optionnel
    variance within groups. Only applies when test is anova_raw.
  • alternative · string · optionnel · two.sided | less | greater | one.sided
    two-sided, or the direction a one-sided test looks in (the raw-unit t and proportion tests take only two.sided or one.sided). Only applies when test is t or t_unequal or two_proportions or two_proportions_unequal or one_proportion or normal_mean or correlation or t_raw or proportions_raw.
  • between_var · number · optionnel
    variance of the group means. Only applies when test is anova_raw.
  • effect_size · string · optionnel · small | medium | large
    Cohen's conventional small, medium or large effect for this test (pwr's cohen.ES), when there is no estimate from data. A convention, not a measurement, and every answer built on it says so. Only applies when test is t or t_unequal or two_proportions or two_proportions_unequal or one_proportion or normal_mean or correlation or chisq or anova or linear_model.

  Exemple d'appel

  {"name": "calculate_power", "arguments": {"test": "t"}}

  Exemple de retour

  {"content": [{"type": "text", "text": "…"}], "structuredContent": {"power": 1, "rCall": "texte", "value": 1, "solved": "texte", "values": "texte", "warnings": "texte", "powerCurve": {}, "wholeUnits": "texte"}}

• calculate_rnaseq_power≈ 1188 tokens

  Sample size and power for an RNA-seq comparison of two groups, one gene at a time: the biological replicates per group needed to detect a fold change at a given sequencing depth and within-group coefficient of variation, or the power, detectable fold change, CV or α a fixed design gives. Leave one of n, cv, effect, alpha and power out (or name it in `solve_for`). Every quantity takes a list, and the answer is the whole grid, so depth against replicates is one call. RNASeqPower 1.52.0 (Hart et al. 2013), reproduced: a negative binomial count with Poisson sequencing noise 1/depth plus biological variance CV².

  Paramètres, retour & exemple (11)

  Paramètres

  • n · array · optionnel
    biological replicates in group 1 (and in group 2, unless `n2` is given).
  • cv · array · optionnel
    the biological coefficient of variation within a group: 0.4 or less for most genes in human studies, about 0.1 in inbred animals (Hart et al.).
  • n2 · array · optionnel
    replicates in group 2, one per `n`. Advanced.
  • cv2 · array · optionnel
    the CV within group 2, one per `cv`. Advanced.
  • alpha · array · optionnel
    α, the two-sided false-positive rate per gene.
  • depth · array · requis
    average depth of coverage of the gene: its expected read count per sample. Hart et al. found most genes at 0.1 per million mapped reads, so 4 at 40 million.
  • power · array · optionnel
    1 − β, the chance of detecting the change if it is real. No default: the target is yours to choose.
  • _files · array · optionnel
    The project: record references shaped like _subject. Their records become library documents a tool names in sequences/parts/document; a trace or alignment is found by file name.
  • effect · array · optionnel
    the fold change to detect; 2 and 0.5 are the same change.
  • _subject · object · optionnel
    The record to act on: exactly one of sequence, accession (+source), sample (an id from list_samples) or file ({name, text} or {name, base64}); record_index picks one record of several.
  • solve_for · string · optionnel · n | cv | effect | alpha | power
    the quantity to solve. Left unset, it is the one of n, cv, effect, alpha and power that was not given. Values: n (n per group), cv (CV), effect (fold change), alpha (α), power (power).

  Exemple d'appel

  {"name": "calculate_rnaseq_power", "arguments": {"depth": []}}

  Exemple de retour

  {"content": [{"type": "text", "text": "…"}], "structuredContent": {"grid": "texte", "curve": {}, "rCall": "texte", "value": 1, "solved": "texte"}}

• call_bases_from_trace≈ 627 tokens

  Call the bases of a Sanger trace from the signal, discarding the instrument's calls and deriving the bases, their positions and their quality from the peaks. The read can come back a DIFFERENT LENGTH than the file's. This ANSWERS the question; `adopt_trace_calls` is what puts the answer onto the read.

  Paramètres, retour & exemple (4)

  Paramètres

  • table · string · optionnel · 3700pop5 | 3700pop6 | 3100pop6 | 3730pop7
    the instrument/polymer calibration table to score against. The same signal scores differently under each, so a quality value is only interpretable with the table named. Defaults to ABI 3730 POP-7.
  • _files · array · optionnel
    The project: record references shaped like _subject. Their records become library documents a tool names in sequences/parts/document; a trace or alignment is found by file name.
  • _subject · object · optionnel
    The record to act on: exactly one of sequence, accession (+source), sample (an id from list_samples) or file ({name, text} or {name, base64}); record_index picks one record of several.
  • document · string · optionnel
    which trace to run on: a file name (`read_F.ab1`) or its project file id. Leave unset to use the trace tab on screen. A file id is project-specific, so a template ships this unset.

  Exemple d'appel

  {"name": "call_bases_from_trace", "arguments": {"table": "3700pop5", "_files": [], "_subject": {}, "document": "texte"}}

  Exemple de retour

  {"content": [{"type": "text", "text": "…"}], "structuredContent": {"bases": 1, "meanQuality": 1, "instrumentBases": 1}}

• call_cq≈ 2468 tokens

  Amplification curves to Cq, one row per reaction. Fits each raw fluorescence curve to a sigmoid (l4-l7, b4-b7), reads the Cq off it under any of the seven definitions (cpD1, cpD2, maxE, expR, Cy0, CQ, maxRatio) or at a fluorescence threshold you set (the classic Ct), and returns the per-reaction efficiency and the fit-quality block beside it, so a bad fit is visible next to the Cq it produced rather than hidden behind it. Also reports the two exponential-phase locators (Tichopad take-off, model midpoint), which come back null rather than 0 when a curve has no exponential phase at all.

  Paramètres, retour & exemple (16)

  Paramètres

  • model · string · optionnel · l4 | l5 | l6 | l7 | b4 | b5 | b6 | b7
    which sigmoid is fitted before a Cq is read off it. Ignored when `auto_model` is on, except as the starting point mselect ranks from. Values: l4 (l4 · 4-param log-logistic), l5 (l5 · + asymmetry), l6 (l6 · + linear baseline drift), l7 (l7 · + quadratic baseline), b4 (b4 · 4-param logistic (raw scale)), b5 (b5 · + asymmetry), b6 (b6 · + linear baseline drift), b7 (b7 · + quadratic baseline).
  • shift · number · optionnel
    cycles added to every reported Cq, for aligning against an instrument's own numbering. Advanced.
  • _files · array · optionnel
    The project: record references shaped like _subject. Their records become library documents a tool names in sequences/parts/document; a trace or alignment is found by file name.
  • curves · string · requis
    the amplification table: a header row, first column the cycle number and every other column one reaction's fluorescence. Tab- or comma-separated, and read by the same parser the Curve->Cq tab uses.
  • amounts · string · optionnel
    the known template amount of each reaction, in column order (comma- or space-separated, `-` for a reaction with none). Each reaction given one reports its calibration factor `cf`, the amount over `init1`, the fit's fluorescence at cycle 0, which is what an absolute quantification scales an unknown's `init1` by. Advanced.
  • _subject · object · optionnel
    The record to act on: exactly one of sequence, accession (+source), sample (an id from list_samples) or file ({name, text} or {name, base64}); record_index picks one record of several.
  • cq_method · string · optionnel · cpD2 | cpD1 | maxE | expR | Cy0 | CQ | maxRatio
    which Cq definition. These are genuinely different quantities, not one number under several names. Values: cpD2 (cpD2 · second-derivative max), cpD1 (cpD1 · first-derivative max), maxE (maxE · cycle of maximum efficiency), expR (expR · exponential region), Cy0 (Cy0 · tangent x-intercept (Guescini)), CQ (CQ · 20 % of the Cq fluorescence), maxRatio (maxRatio · spline, model-free (Shain)).
  • criterion · string · optionnel · ftest | ratio | weights | chisq
    how auto_model ranks. The nested tests are only meaningful inside one family (l4-l7 or b4-b7); AICc weights is the one that can rank all eight. The reduced chi-square needs a measurement error per cycle and the only honest source is the plate's own replicates, so it REFUSES a plate with none. Values: ftest (Nested F-test (within family)), ratio (Likelihood ratio (within family)), weights (AICc weights (all eight models)), chisq (Reduced chi-square (needs replicates)). Only applies when auto_model is true.
  • threshold · number · optionnel
    a fluorescence threshold, on the plate's own fluorescence scale. Set, every Cq is the cycle where the fitted curve crosses it (the classic threshold cycle, Ct) and `cq_method` is overridden. Blank reads the Cq under `cq_method`. A reaction that never reaches it has no Cq and says so.
  • auto_model · boolean · optionnel
    let the plate choose its own model. mselect runs on the FIRST reaction and its winner is applied to every reaction, because Cqs fitted under different models are not comparable — the result reports which model won and the full ranking table.
  • baseline_to · number · optionnel
    last cycle of that window. In cycle. Advanced.
  • baseline_from · number · optionnel
    first cycle of the window the sliwin and LRE estimators scan a baseline over. Affects the all-methods table only: the sigmoidal fit and its Cq do not use a baseline scan. In cycle. Advanced.
  • baseline_scan · number · optionnel
    how many SDs of offset the baseline scan searches; 0 subtracts nothing, which is upstream's own default and is WRONG on real instrument data. Measured against the real LinRegPCR over the 47 reactions of the bundled Own Mix B plate: scanning gives a median efficiency disagreement of 0.038, not scanning gives 0.460. The result reports what the other setting would have returned, so the choice is never hidden. In SD. Advanced.
  • outlier_method · string · optionnel · uni1 | uni2 | multi1 | multi2 | multi3
    which kinetic-outlier test judges the reaction shapes. Two are univariate and three judge a curve's whole shape against a robust MCD covariance of the plate, so a plate can look clean under one and dirty under another. Values: uni1 (Efficiency Z-score (Bar)), uni2 (Shape: cpD1 − cpD2 (Tichopad)), multi1 (Multivariate: cpD1 vs cpD2 residual (Tichopad MOD1)), multi2 (Multivariate: slope, Fmax (Tichopad MOD2)), multi3 (Multivariate: slope, F at cpD1, Fmax (Sisti)). Advanced.
  • max_ratio_smooth · boolean · optionnel
    smooth the raw curve before the maxRatio spline is drawn, as qpcR's `eff(smooth = TRUE)` does. Moves only the `maxRatio` Cq. Only applies when cq_method is maxRatio. Advanced.
  • max_ratio_baseshift · number · optionnel
    fluorescence added to every cycle before the maxRatio spline is drawn. qpcR's own remedy when a baseline near zero makes the cycle-to-cycle ratio explode; it moves only the `maxRatio` Cq. Only applies when cq_method is maxRatio. Advanced.

  Exemple d'appel

  {"name": "call_cq", "arguments": {"curves": "texte"}}

  Exemple de retour

  {"content": [{"type": "text", "text": "…"}], "structuredContent": {"rows": "texte", "count": 1, "model": "texte", "failed": 1, "methods": "texte", "cqMethod": "texte", "outliers": "texte", "errorNote": "texte", "threshold": 1, "modelTable": "texte", "modelChosen": "texte", "outlierStat": "texte"}}

• call_mixed_bases_from_trace≈ 866 tokens

  Call the bases of a Sanger trace AND ask at every position whether a second allele is present, writing a two-base IUB code (R, Y, S, W, K, M) where it is. `mode: het` assumes the two alleles are present in equal amounts, which is the diploid heterozygote case; `mode: mix` assumes nothing about their ratio, for a mixed template, a contaminated read or a pooled sample. The two disagree: on this repo's own corpus they differ on 348 of 5,605 calls. Also returns the ALTERNATIVE calls the search considered and rejected.

  Paramètres, retour & exemple (6)

  Paramètres

  • mode · string · optionnel · het | mix
    het = the two alleles are assumed present 1:1 (a diploid heterozygote); mix = no assumption is made about their ratio.
  • table · string · optionnel · 3700pop5 | 3700pop6 | 3100pop6 | 3730pop7
    the instrument/polymer calibration table to score against. The same signal scores differently under each, so a quality value is only interpretable with the table named. Defaults to ABI 3730 POP-7.
  • _files · array · optionnel
    The project: record references shaped like _subject. Their records become library documents a tool names in sequences/parts/document; a trace or alignment is found by file name.
  • _subject · object · optionnel
    The record to act on: exactly one of sequence, accession (+source), sample (an id from list_samples) or file ({name, text} or {name, base64}); record_index picks one record of several.
  • document · string · optionnel
    which trace to run on: a file name (`read_F.ab1`) or its project file id. Leave unset to use the trace tab on screen. A file id is project-specific, so a template ships this unset.
  • min_ratio · number · optionnel
    how tall a second peak must be, as a fraction of the called peak, before the search will consider it as a second allele. Lowering it widens what is considered, which is not the same as calling more mixed bases.

  Exemple d'appel

  {"name": "call_mixed_bases_from_trace", "arguments": {"mode": "het", "table": "3700pop5", "_files": [], "_subject": {}, "document": "texte", "min_ratio": 1}}

  Exemple de retour

  {"content": [{"type": "text", "text": "…"}], "structuredContent": {"bases": 1, "mixedBases": 1, "meanQuality": 1, "instrumentBases": 1}}

• cancel_research_run≈ 643 tokens

  Withdraw a research run's pending hypotheses (all of them, or the ones named) so no resume runs them, and return the sealed run file. Nothing is deleted: a canceled hypothesis stays registered and still counts in e-BH with e 1, because it was registered before any result and dropping it would raise the others' chance of support after the fact. Answered and settled hypotheses cannot be canceled. To stop a run that is advancing in budgeted slices, stop calling resume_research_run; cancel when the pending hypotheses should never run.

  Paramètres, retour & exemple (5)

  Paramètres

  • run · object · requis
    the run file to cancel pending hypotheses in.
  • _files · array · optionnel
    The project: record references shaped like _subject. Their records become library documents a tool names in sequences/parts/document; a trace or alignment is found by file name.
  • reason · string · optionnel
    why, recorded on each canceled attempt.
  • _subject · object · optionnel
    The record to act on: exactly one of sequence, accession (+source), sample (an id from list_samples) or file ({name, text} or {name, base64}); record_index picks one record of several.
  • hypotheses · array · optionnel
    the pending hypotheses to cancel, by id; unset cancels every pending one.

  Exemple d'appel

  {"name": "cancel_research_run", "arguments": {"run": {}}}

  Exemple de retour

  {"content": [{"type": "text", "text": "…"}], "structuredContent": {"run": "texte", "status": "texte", "cancelled": "texte"}}

• canonical_tautomer≈ 595 tokens

  A small molecule's tautomers and the canonical one, as RDKit's TautomerEnumerator finds and scores them: 37 hydrogen-shift transforms (after MolVS and Sitzmann 2010), scored by aromatic rings, twelve weighted groups and hydrogens on P, S, Se and Te, ties to the smaller SMILES. Returns every tautomer, the canonical SMILES, the score and the 0-based atoms (implicit hydrogens, molfile order) a hydrogen moved between.

  Paramètres, retour & exemple (5)

  Paramètres

  • _files · array · optionnel
    The project: record references shaped like _subject. Their records become library documents a tool names in sequences/parts/document; a trace or alignment is found by file name.
  • _subject · object · optionnel
    The record to act on: exactly one of sequence, accession (+source), sample (an id from list_samples) or file ({name, text} or {name, base64}); record_index picks one record of several.
  • molecule · string · requis
    the structure: SMILES or a molfile.
  • max_tautomers · number · optionnel
    stop the enumeration at this many tautomers.
  • max_transforms · number · optionnel
    stop after this many transform applications.

  Exemple d'appel

  {"name": "canonical_tautomer", "arguments": {"molecule": "texte"}}

  Exemple de retour

  {"content": [{"type": "text", "text": "…"}], "structuredContent": {"summary": "texte", "canonical": "texte", "tautomers": "texte"}}

• check_assay_decay≈ 1022 tokens

  Check a published PCR or sequencing assay against the sequences that are circulating now: for each oligo, where its best binding site is in each genome, how many positions mismatch, and whether a mismatch sits in the 3′ end a polymerase has to extend through. It answers the question an assay's age raises — the design was made against the genomes available on the day, and the target has drifted under it since — as a RATE per oligo with an exact binomial interval, plus the mismatch count at each position of the oligo, which is the shape a manufacturer's own in-silico inclusivity table takes. IUPAC codes in an oligo are read as the breadth its designers meant, so a position a code covers is never a mismatch; a site overlapping ambiguous bases in a submitted assembly is missing data and leaves that genome out of that oligo's denominator rather than counting as a match or a mismatch. A probe gets no 3′-end rate, because it is not extended. Graded against EMBOSS fuzznuc on every oligo of twelve published SARS-CoV-2 assays over 400 genomes.

  Paramètres, retour & exemple (8)

  Paramètres

  • assay · string · optionnel
    what the assay is called, for the result to name.
  • _files · array · optionnel
    The project: record references shaped like _subject. Their records become library documents a tool names in sequences/parts/document; a trace or alignment is found by file name.
  • probes · array · optionnel
    the assay's probes, 5′→3′. Scored the same way but with no 3′-end rule: a probe is not extended.
  • primers · array · optionnel
    the assay's primers, 5′→3′, IUPAC allowed. Written `name=SEQUENCE` to carry the published name.
  • _subject · object · optionnel
    The record to act on: exactly one of sequence, accession (+source), sample (an id from list_samples) or file ({name, text} or {name, base64}); record_index picks one record of several.
  • sequences · array · requis
    the genomes to check against: wire upstream records here, or list library document names.
  • include_subject · boolean · optionnel
    also check the node's subject (the open or wired record).
  • three_prime_window · number · optionnel
    how many bases from a primer's 3′ end count as its 3′ end. 5 is the window Primer-BLAST's own specificity rule uses. In bp.

  Exemple d'appel

  {"name": "check_assay_decay", "arguments": {"sequences": []}}

  Exemple de retour

  {"content": [{"type": "text", "text": "…"}], "structuredContent": {"sites": "texte", "worst": "texte", "oligos": "texte", "result": "texte", "worstRate": 1, "threePrime": 1}}

• check_color_balance≈ 768 tokens

  Will the sequencer SEE these indexes? Per-cycle channel occupancy for a set of index sequences under an instrument's own SBS chemistry, checked against Illumina's rules (no dark cycle, both channels preferred, no GG in the first two cycles), each violation citing the vendor article it comes from — and the same set scored across EVERY chemistry generation at once, because XLEAP moved the dual-color base from A to C and a set balanced on a NovaSeq 6000 is not balanced on a NovaSeq X. This is the color question alone; check_index_pool asks it alongside distance, duplicates and hopping for a whole pool.

  Paramètres, retour & exemple (4)

  Paramètres

  • _files · array · optionnel
    The project: record references shaped like _subject. Their records become library documents a tool names in sequences/parts/document; a trace or alignment is found by file name.
  • _subject · object · optionnel
    The record to act on: exactly one of sequence, accession (+source), sample (an id from list_samples) or file ({name, text} or {name, base64}); record_index picks one record of several.
  • barcodes · array · requis
    the index sequences to score, one per sample.
  • instrument · string · optionnel · iSeq 100 | MiniSeq | MiniSeq Rapid kits | NextSeq 500/550 | NextSeq 1000/2000 | NovaSeq 6000 | NovaSeq X / X Plus | MiSeq
    the instrument whose chemistry the set is judged under, and whose index-2 orientation applies.

  Exemple d'appel

  {"name": "check_color_balance", "arguments": {"barcodes": []}}

  Exemple de retour

  {"content": [{"type": "text", "text": "…"}], "structuredContent": {"ok": true, "tier": "texte", "cycles": "texte", "violations": "texte", "acrossChemistries": "texte"}}

• check_golden_gate_parts≈ 648 tokens

  Check parts BEFORE a Type-IIS assembly: how many recognition sites each carries, which of them are the two deliberate flanking sites and which are internal sites that will mis-cut the part. This is what answers “why will this assembly not work” — an internal site has to be domesticated (silently recoded) before the reaction can be trusted.

  Paramètres, retour & exemple (5)

  Paramètres

  • parts · array · optionnel
    the parts to check — wire upstream `record` outputs here, or list library document names/ids.
  • _files · array · optionnel
    The project: record references shaped like _subject. Their records become library documents a tool names in sequences/parts/document; a trace or alignment is found by file name.
  • enzyme · string · optionnel
    the Type-IIS enzyme the assembly will use.
  • _subject · object · optionnel
    The record to act on: exactly one of sequence, accession (+source), sample (an id from list_samples) or file ({name, text} or {name, base64}); record_index picks one record of several.
  • include_subject · boolean · optionnel
    also check the node's subject.

  Exemple d'appel

  {"name": "check_golden_gate_parts", "arguments": {"parts": [], "_files": [], "enzyme": "texte", "_subject": {}, "include_subject": true}}

  Exemple de retour

  {"content": [{"type": "text", "text": "…"}], "structuredContent": {"parts": "texte", "ready": true, "internalSiteCount": 1, "needsDomestication": "texte"}}

• check_index_pool≈ 1590 tokens

  Will this pool of sample indexes actually sequence? One verdict over the indexes a lab is about to load: duplicates, uniform length, the distance the set really guarantees against the distance it claims, per-cycle color balance on the chosen instrument's own chemistry, the index-2 orientation that instrument reads, and index-hopping exposure — how many i7 x i5 combinations exist against how many are in use, and which swaps would turn one sample's read into another's undetectably. Takes a pasted list or a vendor kit by id. It CHECKS a pool; design_barcodes builds one.

  Paramètres, retour & exemple (10)

  Paramètres

  • kit · string · optionnel · | truseq-single-indexes | truseq-cd-indexes | idt-truseq-ud-indexes | idt-illumina-ud-plate-a | idt-illumina-ud-plate-b | idt-illumina-ud-plate-c | idt-illumina-ud-plate-d
    a vendor kit id instead of a pasted list — the kit's own indexes are resolved and checked. Ignored when `pool` is given. Values: (No kit — paste a list instead), truseq-single-indexes (TruSeq Single Indexes — Illumina, 24 indexes), truseq-cd-indexes (TruSeq DNA and RNA CD Indexes — Illumina, 96 indexes), idt-truseq-ud-indexes (IDT for Illumina–TruSeq DNA and RNA UD Indexes — Illumina / IDT, 100 indexes), idt-illumina-ud-plate-a (IDT for Illumina UD Indexes, Plate A/Set 1 — Illumina / IDT, 96 indexes), idt-illumina-ud-plate-b (IDT for Illumina UD Indexes, Plate B/Set 2 — Illumina / IDT, 96 indexes), idt-illumina-ud-plate-c (IDT for Illumina UD Indexes, Plate C/Set 3 — Illumina / IDT, 98 indexes), idt-illumina-ud-plate-d (IDT for Illumina UD Indexes, Plate D/Set 4 — Illumina / IDT, 100 indexes). Only applies when pool is not given.
  • pool · string · optionnel
    the pool as text — one row per sample: `name<TAB>i7[<TAB>i5]`, or bare index sequences one per line, with or without a header. Rows that cannot be read are REPORTED with their line number, never dropped.
  • _files · array · optionnel
    The project: record references shaped like _subject. Their records become library documents a tool names in sequences/parts/document; a trace or alignment is found by file name.
  • metric · string · optionnel · hamming | seqlev | levenshtein
    error model the distance guarantee is measured under — a pool safe under substitutions may be unsafe under indels. Values: hamming (Hamming (substitutions)), seqlev (Sequence-Levenshtein (indels)), levenshtein (Levenshtein).
  • _subject · object · optionnel
    The record to act on: exactly one of sequence, accession (+source), sample (an id from list_samples) or file ({name, text} or {name, base64}); record_index picks one record of several.
  • i5_cycles · number · optionnel
    index-2 read length from the run recipe. 0 = use the indexes' own length.
  • i7_cycles · number · optionnel
    index-1 read length from the RUN RECIPE, when it differs from the index length — a 10 nt index read at 8 cycles is an 8 nt index for every purpose here. 0 = use the indexes' own length.
  • instrument · string · optionnel · iSeq 100 | MiniSeq | MiniSeq Rapid kits | NextSeq 500/550 | NextSeq 1000/2000 | NovaSeq 6000 | NovaSeq X / X Plus | MiSeq
    which instrument the run is on. It decides the chemistry the color balance is judged under AND the orientation index 2 is read in — a pool balanced on a NovaSeq 6000 is not balanced on a NovaSeq X.
  • library_prep · string · optionnel · patterned-examp | truseq-pcr-free
    which of Illumina's published hopping-rate classes applies. The check multiplies the published RANGE by what this pool can throw away, to report how much is unrecoverable — it never predicts a rate for your run. Values: patterned-examp (Patterned flow cell, ExAmp chemistry), truseq-pcr-free (TruSeq PCR-Free libraries).
  • required_distance · number · optionnel
    the minimum distance the pool is SUPPOSED to guarantee, if it was designed to one — the check says whether it does. 0 = report the distance without judging it. Advanced.

  Exemple d'appel

  {"name": "check_index_pool", "arguments": {"kit": "", "pool": "texte", "_files": [], "metric": "hamming", "_subject": {}, "i5_cycles": 1}}

  Exemple de retour

  {"content": [{"type": "text", "text": "…"}], "structuredContent": {"reads": "texte", "checks": "texte", "hopping": "texte", "samples": 1, "skipped": "texte", "verdict": "texte", "failures": 1, "guarantee": "texte", "closestPairs": "texte"}}

• check_invariants≈ 991 tokens

  Decide whether a sequence is scientifically admissible: protein unchanged, forbidden restriction sites absent, reading frame intact, length/GC/CAI inside stated bounds. Every verdict names what broke, where, and the remedy. Run this after any design or optimisation step, and stop the chain when `admissible` is false — never report a designed sequence without it.

  Paramètres, retour & exemple (16)

  Paramètres

  • table · number · optionnel
    NCBI translation table. Advanced.
  • _files · array · optionnel
    The project: record references shaped like _subject. Their records become library documents a tool names in sequences/parts/document; a trace or alignment is found by file name.
  • max_gc · number · optionnel
    maximum GC fraction (0-1).
  • min_gc · number · optionnel
    minimum GC fraction (0-1).
  • min_cai · number · optionnel
    minimum CAI (needs cai_organism). Advanced.
  • _subject · object · optionnel
    The record to act on: exactly one of sequence, accession (+source), sample (an id from list_samples) or file ({name, text} or {name, base64}); record_index picks one record of several.
  • sequence · string · optionnel
    the sequence to judge — defaults to the open record.
  • gc_window · number · optionnel
    judge every window of this many bases instead of the whole sequence — a synthesis is rejected on a local GC peak, not on the mean. In bp. Advanced.
  • max_length · number · optionnel
    maximum length [bp]. In bp. Advanced.
  • min_length · number · optionnel
    minimum length [bp]. In bp. Advanced.
  • cai_organism · string · optionnel
    host for the codon-adaptation check, e.g. sce. Advanced.
  • forbid_sites · array · optionnel
    enzyme names that must not cut, e.g. BsaI, BsmBI.
  • require_stop · boolean · optionnel
    with require_frame: the last codon must be a stop. Only applies when require_frame is true. Advanced.
  • require_frame · boolean · optionnel
    length divisible by 3 and no premature stop.
  • require_start · boolean · optionnel
    with require_frame: the first codon must be a start codon. Only applies when require_frame is true. Advanced.
  • preserve_protein_of · string · optionnel
    the ORIGINAL coding sequence (or its protein): the result must still translate to it.

  Exemple d'appel

  {"name": "check_invariants", "arguments": {"table": 1, "_files": [], "max_gc": 1, "min_gc": 1, "min_cai": 1, "_subject": {}}}

  Exemple de retour

  {"content": [{"type": "text", "text": "…"}], "structuredContent": {"failed": 1, "checked": 1, "summary": "texte", "verdicts": "texte", "admissible": true}}

• check_manufacturability≈ 1209 tokens

  Measure a sequence against what a NAMED synthesis vendor publishes it can make: length, average and windowed GC, homopolymer runs, tandem repeats, long repeats and hairpin-forming inverted repeats. Every threshold is the vendor's own, read from the vendor's own page with the date it was read, and every finding carries the span it is about so it can be drawn. It reports the limits that are MET as well as the ones exceeded, because a list of failures cannot tell a clean sequence from an unchecked one. It never predicts a synthesis outcome and never rules a sequence out: a vendor publishes what it supports, so being outside a published window is a conversation with the supplier, not a rejection.

  Paramètres, retour & exemple (5)

  Paramètres

  • _files · array · optionnel
    The project: record references shaped like _subject. Their records become library documents a tool names in sequences/parts/document; a trace or alignment is found by file name.
  • vendor · string · optionnel · idt-gblocks | idt-eblocks | twist-clonal | twist-fragments
    which vendor product to measure against. Each carries its own limits, and two vendors can honestly disagree about one sequence. Values: idt-gblocks (IDT gBlocks Gene Fragments), idt-eblocks (IDT eBlocks Gene Fragments), twist-clonal (Twist Bioscience Clonal Genes), twist-fragments (Twist Bioscience Gene Fragments).
  • feature · string · optionnel
    measure a named feature of the open record instead of the whole thing — the insert you are about to order rather than the vector it sits in. Advanced.
  • _subject · object · optionnel
    The record to act on: exactly one of sequence, accession (+source), sample (an id from list_samples) or file ({name, text} or {name, base64}); record_index picks one record of several.
  • sequence · string · optionnel
    the sequence to measure. Leave unset to use the open record, or the current selection when there is one.

  Exemple d'appel

  {"name": "check_manufacturability", "arguments": {"_files": [], "vendor": "idt-gblocks", "feature": "texte", "_subject": {}, "sequence": "texte"}}

  Exemple de retour

  {"content": [{"type": "text", "text": "…"}], "structuredContent": {"spans": "texte", "checked": 1, "outside": 1, "profile": "texte", "reading": "texte", "verdict": "texte", "findings": "texte", "notGraded": "texte", "repeatScreens": "texte"}}

• check_methylation_block≈ 694 tokens

  Whether the host's own methylation blocks the given enzymes ON THIS PLASMID, from REBASE's methylation-sensitivity tables localised onto your sites. The other term of the same reaction question `find_star_sites` answers. It is deliberately per-SITE and not per-enzyme: REBASE says Dam blocks ClaI, and pBR322's single ClaI site carries no overlapping GATC, so the enzyme-level warning does not apply there. An enzyme REBASE has never examined comes back `examined: false`, which is UNTESTED and never a clearance.

  Paramètres, retour & exemple (3)

  Paramètres

  • _files · array · optionnel
    The project: record references shaped like _subject. Their records become library documents a tool names in sequences/parts/document; a trace or alignment is found by file name.
  • enzymes · array · requis
    enzymes to check — resolved against the bundled cut catalog (REBASE spellings; smaller than the REBASE dossier the editor shows). Left unset, the run uses your active enzyme collection.
  • _subject · object · optionnel
    The record to act on: exactly one of sequence, accession (+source), sample (an id from list_samples) or file ({name, text} or {name, base64}); record_index picks one record of several.

  Exemple d'appel

  {"name": "check_methylation_block", "arguments": {"enzymes": []}}

  Exemple de retour

  {"content": [{"type": "text", "text": "…"}], "structuredContent": {"blocked": 1, "enzymes": "texte", "unexamined": 1, "blockedEnzymes": "texte"}}

• check_primer_specificity≈ 996 tokens

  Check primer pairs for products off their template, the way NCBI Primer-BLAST does, and rank them by it: each distinct primer is searched against a sequence database at EMBL-EBI with short-query BLAST, hits are paired into products by Primer-BLAST's own mismatch rule, and the template is searched too so the record identical to it is recognized as the intended target. Pairs with no product elsewhere rank first, in the order given, then pairs not checked, then pairs with a named unintended product. Primer sequences and the template LEAVE THE MACHINE; the database is a collection, not an assembled genome, and cannot be filtered by organism.

  Paramètres, retour & exemple (9)

  Paramètres

  • email · string · optionnel
    EBI requires a contact address on every submission (their abuse contact, not a login). Left empty, the one saved in any EMBL-EBI panel is used.
  • pairs · string · optionnel
    several pairs to rank, one per line as `forward reverse` (whitespace or a comma between), in their design order. Taken instead of forward/reverse when given.
  • top_n · number · optionnel
    how many of the pairs, from the top, to search. The rest rank as unchecked. At most 14, so the batch stays inside EMBL-EBI's 30 searches.
  • _files · array · optionnel
    The project: record references shaped like _subject. Their records become library documents a tool names in sequences/parts/document; a trace or alignment is found by file name.
  • forward · string · optionnel
    one pair's forward primer, 5'→3' (wire design_primers' `forward`).
  • reverse · string · optionnel
    that pair's reverse primer, 5'→3' (wire design_primers' `reverse`).
  • _subject · object · optionnel
    The record to act on: exactly one of sequence, accession (+source), sample (an id from list_samples) or file ({name, text} or {name, base64}); record_index picks one record of several.
  • database · string · optionnel
    the nucleotide database id, as the service names it (em_all, em_rel_hum…). Left empty, the service's OWN nucleotide default is used and reported back.
  • template · string · optionnel
    the sequence the pairs were designed on. Searched too: the database record identical to it is where the intended product lives. Left empty, the open record is used; with neither, every product counts as unintended and the result says so.

  Exemple d'appel

  {"name": "check_primer_specificity", "arguments": {"email": "texte", "pairs": "texte", "top_n": 1, "_files": [], "forward": "texte", "reverse": "texte"}}

  Exemple de retour

  {"content": [{"type": "text", "text": "…"}], "structuredContent": {"ranked": "texte", "forward": "texte", "reverse": "texte", "identical": "texte", "specificCount": 1}}

• check_rows≈ 1185 tokens

  A QC gate over a TABLE: assert something about every row at once (every band inside a size window, no guide above an off-target score, at least three assays under a penalty). Fails the pipeline (so everything downstream skips) and names the rows that broke the rule.

  Paramètres, retour & exemple (15)

  Paramètres

  • max · number · optionnel
    upper bound, inclusive. Only applies when operator is between.
  • min · number · optionnel
    lower bound, inclusive. Only applies when operator is between.
  • set · array · optionnel
    the values the field must be one of (or none of). Only applies when operator is in or not_in.
  • text · string · optionnel
    the text the field must contain. Only applies when operator is contains.
  • count · number · optionnel
    N, for the counted requirements. Only applies when require is at_least or at_most or exactly.
  • field · string · optionnel
    which field of each row to test (e.g. `size`, `score`). Leave empty when the rows are plain numbers.
  • items · array · requis
    the rows to check. Wire a json/list output (bands, guides, assays, amplicons).
  • label · string · optionnel
    what this gate is checking, in your words. It becomes the message when it fails.
  • value · number · optionnel
    the value to compare against. Only applies when operator is == or != or > or >= or < or <=.
  • _files · array · optionnel
    The project: record references shaped like _subject. Their records become library documents a tool names in sequences/parts/document; a trace or alignment is found by file name.
  • record · string · optionnel
    optional: the record this gate is guarding. It comes back out of `record` when the check passes, so the gate sits in the middle of a chain.
  • require · string · optionnel · all | any | none | at_least | at_most | exactly
    what must hold across the table. Values: all (every row), any (at least one row), none (no row), at_least (at least N rows), at_most (at most N rows), exactly (exactly N rows).
  • _subject · object · optionnel
    The record to act on: exactly one of sequence, accession (+source), sample (an id from list_samples) or file ({name, text} or {name, base64}); record_index picks one record of several.
  • operator · string · optionnel · == | != | > | >= | < | <= | between | in
    how each row is compared. Values: == (equals), != (does not equal), > (greater than), >= (at least), < (less than), <= (at most), between (between (inclusive)), in (is one of), not_in (is none of), contains (contains text), is_true (is true), not_empty (is not empty).
  • report_only · boolean · optionnel
    report the verdict instead of stopping the run: wire `passed` (or `failed`) into another step's condition to choose a branch.

  Exemple d'appel

  {"name": "check_rows", "arguments": {"items": []}}

  Exemple de retour

  {"content": [{"type": "text", "text": "…"}], "structuredContent": {"failed": true, "passed": true, "record": {}, "matched": 1, "message": "texte", "offenders": "texte"}}

• check_scorpion_stem≈ 1805 tokens

  A Scorpion probe's two melting temperatures, side by side: the stem-loop's own hairpin and the duplex the loop makes with its target on the amplicon. A Scorpion is a primer carrying a stem-loop probe on a non-amplifiable blocker (Whitcombe 1999), and it reports by the loop finding its target and pulling the stem apart - so the design question is a RELATION between those two structures, not a property of either. Returns both temperatures, their difference, the stem's GC, and a verdict against WHATEVER margin you pass. It does not apply a margin of its own authority: the widely-quoted 5-10 °C figure comes from one design tool's tech note and has no primary citation, so the default is labelled as that rule of thumb and every result says which margin produced its verdict.

  Paramètres, retour & exemple (7)

  Paramètres

  • probe · string · requis
    the whole probe element, 5' stem arm + loop + 3' stem arm. The element is what folds, so it is what the structure engine is given - the loop alone would compute a hairpin the molecule does not have.
  • _files · array · optionnel
    The project: record references shaped like _subject. Their records become library documents a tool names in sequences/parts/document; a trace or alignment is found by file name.
  • margin · number · optionnel
    how many °C the stem Tm must exceed the loop-target Tm for the verdict to pass. Yours to set: the 5-10 °C rule of thumb this defaults to the floor of is a design tool's, not a measured value from the primary literature. In °C.
  • target · string · requis
    the loop's target on the amplicon, 5'->3'. This is the OTHER temperature: a Scorpion opens because the loop finds this, so it is the loop-target duplex that has to be stable, not the loop's own self-structure.
  • _subject · object · optionnel
    The record to act on: exactly one of sequence, accession (+source), sample (an id from list_samples) or file ({name, text} or {name, base64}); record_index picks one record of several.
  • conditions · object · optionnel
    salt, magnesium, dNTP and oligo concentrations plus the salt-correction method the stem Tm is measured in. Left unset it is filled from your reaction-conditions settings, and falls back to primer3's defaults when there are none. Advanced.
  • stem_length · number · optionnel
    how many bases of the 5' end form the stem arm. Reported back rather than guessed. The two vendors disagree on the range - LGC Biosearch, who sell Scorpions, publish 5-7 nt and PremierBiosoft's design tool says 6-7 - so neither is enforced. In nt.

  Exemple d'appel

  {"name": "check_scorpion_stem", "arguments": {"probe": "texte", "target": "texte"}}

  Exemple de retour

  {"content": [{"type": "text", "text": "…"}], "structuredContent": {"notes": "texte", "stemTm": 1, "probeTm": 1, "difference": 1, "clearsMargin": "texte", "marginSource": "texte", "stemGcPercent": 1}}

• check_value≈ 1245 tokens

  A QC gate. Compares a wired value against a threshold and PASSES or FAILS the pipeline there — every node downstream of a failed gate is skipped, so a run stops at the first check that does not hold. This is how a pipeline expresses 'only continue if the clone is right'.

  Paramètres, retour & exemple (15)

  Paramètres

  • max · number · optionnel
    upper bound, inclusive. Only applies when operator is between.
  • min · number · optionnel
    lower bound, inclusive. Only applies when operator is between.
  • set · array · optionnel
    the values the checked value must be one of (or none of), compared as text, so `1` matches 1. Only applies when operator is in or not_in.
  • text · string · optionnel
    the text the value must contain. Only applies when operator is contains.
  • label · string · optionnel
    what this gate is checking, in your words — it becomes the message when the gate fails (e.g. 'single EcoRI site').
  • value · number · requis
    the value to check — wire a number (cut count, product size, tip count, Tm) or any output; a list is compared by its length.
  • _files · array · optionnel
    The project: record references shaped like _subject. Their records become library documents a tool names in sequences/parts/document; a trace or alignment is found by file name.
  • record · string · optionnel
    optional: the record this gate is guarding. It comes straight back out of the `record` output when the check passes, so the gate sits in the middle of a chain.
  • against · number · optionnel
    optional: compare against another step's value instead of the fixed threshold. When wired, this wins over `threshold`. Only applies when operator is == or != or > or >= or < or <=.
  • _subject · object · optionnel
    The record to act on: exactly one of sequence, accession (+source), sample (an id from list_samples) or file ({name, text} or {name, base64}); record_index picks one record of several.
  • operator · string · optionnel · == | != | > | >= | < | <= | between | in
    how to compare. Values: == (equals), != (does not equal), > (greater than), >= (at least), < (less than), <= (at most), between (between (inclusive)), in (is one of), not_in (is none of), contains (contains text), is_true (is true), not_empty (is not empty).
  • threshold · number · optionnel
    the value to compare against. Leave it unset and wire `against` instead to compare two steps. Only applies when operator is == or != or > or >= or < or <=.
  • report_only · boolean · optionnel
    report the verdict instead of stopping the run: wire `passed` (or `failed`) into another step's condition to choose a branch.
  • against_factor · number · optionnel
    multiply the compared-against value by this first, so `at least twice the smallest band` is one gate rather than an arithmetic step. Only applies when operator is == or != or > or >= or < or <=.
  • against_offset · number · optionnel
    then add this, so `within 50 bp of the predicted size` is expressible against a computed value. Only applies when operator is == or != or > or >= or < or <=.

  Exemple d'appel

  {"name": "check_value", "arguments": {"value": 1}}

  Exemple de retour

  {"content": [{"type": "text", "text": "…"}], "structuredContent": {"value": "texte", "failed": true, "passed": true, "record": {}, "message": "texte"}}

• classify_droplets≈ 2779 tokens

  ddPCR droplet amplitudes to populations. For TWO targets, a four-way classification — NN, NP, PN, PP — under any of THREE published methods that answer different questions and none of which is a fallback for another. `grid` applies eight fixed thresholds: reproducible and auditable, the only one that does not move when the data does, and the only one that needs someone to have chosen the numbers. `kmeans` clusters both channels at once and names the clusters by where they sit, so it adapts to the well, and it CANNOT abstain because k-means partitions everything. `knn` classifies against a well you have already labelled and abstains into `Rain` when the neighbour vote is weaker than a floor you set, so it is the only one that can decline per droplet. They disagree on the droplets between the populations, and that disagreement is the honest measure of how much an answer rests on the method rather than on the data. Distinct from `gate_droplets`, which asks whether a droplet is EMPTY per channel and ends in a concentration; this asks which of four populations it belongs to. For ONE to FOUR targets multiplexed by amplitude, ddPCRclust names up to sixteen populations from the primary clusters and reports each target's copies per droplet, by any of three first clusterings or their consensus: `density` places the primaries from density gates, `samspectral` from spectral clustering of a faithful sample, `flowpeaks` from the density peaks k-means clusters climb to, and `ensemble` (ddPCRclust's own default) runs all three and keeps the partition that agrees most with the others, with their mean corrected Rand index as the confidence. A plate of exports with ddPCRclust's run template is classified well by well and can be normalised to a constant control.

  Paramètres, retour & exemple (22)

  Paramètres

  • k · number · optionnel
    for `knn`: how many nearest labelled neighbours vote. Only applies when method is knn.
  • prob · number · optionnel
    for `knn`: the smallest winning share of the vote that counts as a call. Below it the droplet is `Rain`. 0 disables the floor. At k = 5 a bare 3-2 majority is 0.6, so any floor at or below 0.5 accepts every droplet the vote decided at all. Only applies when method is knn.
  • _files · array · optionnel
    The project: record references shaped like _subject. Their records become library documents a tool names in sequences/parts/document; a trace or alignment is found by file name.
  • ch1_nn · number · optionnel
    grid: Ch1 below this and Ch2 below `ch2_nn` is NN. Only applies when method is grid.
  • ch1_np · number · optionnel
    grid: Ch1 below this and Ch2 above `ch2_np` is NP. Only applies when method is grid.
  • ch1_pn · number · optionnel
    grid: Ch1 above this and Ch2 below `ch2_pn` is PN. Only applies when method is grid.
  • ch1_pp · number · optionnel
    grid: Ch1 above this and Ch2 above `ch2_pp` is PP. Only applies when method is grid.
  • ch2_nn · number · optionnel
    grid: the Ch2 half of the NN box. Only applies when method is grid.
  • ch2_np · number · optionnel
    grid: the Ch2 half of the NP box. Only applies when method is grid.
  • ch2_pn · number · optionnel
    grid: the Ch2 half of the PN box. Only applies when method is grid.
  • ch2_pp · number · optionnel
    grid: the Ch2 half of the PP box. Only applies when method is grid.
  • method · string · optionnel · grid | kmeans | knn | density | samspectral | flowpeaks | ensemble
    which classifier. `grid` needs its eight thresholds to suit your assay; `kmeans` needs nothing and cannot abstain; `knn` needs `training` and is the only one that can leave a droplet unassigned; `density`, `samspectral`, `flowpeaks` and `ensemble` (ddPCRclust) are for one to four targets and name populations by marker number (`1`, `1+2`, ...); `ensemble` runs the other three and is the slowest.
  • markers · string · optionnel
    for `density`: the well's four marker slots, comma-separated, as in ddPCRclust's run template. A name is a target the reaction carries; an EMPTY slot is one it does not, so `a,,c,d` is a three-target well whose cluster 2 is missing. The number of names is the number of targets. Only applies when method is density or samspectral or flowpeaks or ensemble.
  • _subject · object · optionnel
    The record to act on: exactly one of sequence, accession (+source), sample (an id from list_samples) or file ({name, text} or {name, base64}); record_index picks one record of several.
  • droplets · string · requis
    the well to classify: two amplitude columns, `Ch1` then `Ch2`, one row per droplet. A header line is optional. This is the whole well, not a summary. For the ddPCRclust methods it may instead be a PLATE: each export as `# <file name>` then its CSV, separated by a line of `---`, the well id read from the file name (`..._B01_Amplitude.csv`).
  • sam_seed · number · optionnel
    for `samspectral` and `ensemble`: R's `set.seed` before the run. SamSPECTRAL keeps the best of 1000 k-means starts drawn from it, and on a plate one stream runs through the wells in order, as `ddPCRclust()` does. Only applies when method is samspectral or ensemble.
  • template · string · optionnel
    for a PLATE under the ddPCRclust methods: ddPCRclust's run template (a `>name, channel1=..., channel2=..., description` line, then `Well,Sample type,# of markers,Marker 1..Marker 4`). Each well then takes its own row's markers instead of `markers`. Only applies when method is density or samspectral or flowpeaks or ensemble.
  • training · string · optionnel
    for `knn` only: an already-labelled well, as `Ch1,Ch2,class` with class one of NN, NP, PN, PP or Rain. Rain IS a class here and not a rejection — a droplet can be assigned to it on the strength of its neighbours, separately from the probability floor below. Only applies when method is knn.
  • random_seed · number · optionnel
    for `knn`: ties among equidistant neighbours, and among tied winning classes, are broken from this stream. On a well-separated plate it changes nothing; where droplets sit exactly between populations it does, and a deterministic tie-break would be stable and wrong. Only applies when method is knn.
  • sensitivity · number · optionnel
    for `density`: how finely the initial cluster search resolves density peaks (its step is 0.02 / sensitivity³). Higher divides the data into more clusters, lower merges more. Only applies when method is density or samspectral or flowpeaks or ensemble.
  • distance_param · number · optionnel
    for `density`: the share of the path between two clusters within which rain goes to the LOWER one; the rest goes to the higher one. Only applies when method is density or samspectral or flowpeaks or ensemble.
  • constant_control · string · optionnel
    for a PLATE under the ddPCRclust methods: the marker that should read the same in every well. Every well's copies per droplet are multiplied by the control's highest value on the plate over its own, as `calculateCPDs(constantControl =)` does. Empty: no normalisation. Only applies when method is density or samspectral or flowpeaks or ensemble.

  Exemple d'appel

  {"name": "classify_droplets", "arguments": {"droplets": "texte"}}

  Exemple de retour

  {"content": [{"type": "text", "text": "…"}], "structuredContent": {"total": 1, "wells": "texte", "counts": "texte", "method": "texte", "params": "texte", "centres": "texte", "classes": "texte", "members": "texte", "confidence": 1, "normalised": "texte", "copies_per_droplet": "texte"}}

• classify_grammar_part≈ 724 tokens

  Which Golden Braid / MoClo / Yeast ToolKit grammar, position and level the open plasmid represents (or null). Reads the record's own annotations, which is what lets an assembled transcription unit be recognised by its backbone half, and what lets a Level-0 module whose own backbone carries an extra site for the release enzyme be told from that backbone. Configured entry vectors are a Parts Bin concept and are NOT available here, so a TU sitting in a named acceptor is reported by its overhangs rather than by that acceptor's name.

  Paramètres, retour & exemple (2)

  Paramètres

  • _files · array · optionnel
    The project: record references shaped like _subject. Their records become library documents a tool names in sequences/parts/document; a trace or alignment is found by file name.
  • _subject · object · optionnel
    The record to act on: exactly one of sequence, accession (+source), sample (an id from list_samples) or file ({name, text} or {name, base64}); record_index picks one record of several.

  Exemple d'appel

  {"name": "classify_grammar_part", "arguments": {"_files": [], "_subject": {}}}

  Exemple de retour

  {"content": [{"type": "text", "text": "…"}], "structuredContent": {"level": 1, "spans": "texte", "grammar": "texte", "isVector": true, "position": "texte", "releaseCuts": 1, "releaseEnzyme": "texte", "classification": "texte"}}

• cluster_molecules≈ 746 tokens

  Cluster or diversity-pick a list of small molecules on 1 − Tanimoto of Morgan radius-2 fingerprints: Butina sphere exclusion (RDKit ClusterData, optional reordering), MaxMin diversity picking (RDKit MaxMinPicker, seeded), or average linkage (UPGMA) cut into k clusters. Indices are 0-based.

  Paramètres, retour & exemple (9)

  Paramètres

  • seed · number · optionnel
    MaxMin: seed of the first pick, as RDKit's seed.
  • picks · number · optionnel
    MaxMin: how many structures to pick.
  • _files · array · optionnel
    The project: record references shaped like _subject. Their records become library documents a tool names in sequences/parts/document; a trace or alignment is found by file name.
  • method · string · optionnel · butina | maxmin | average
    the clustering method. Values: butina (Butina (sphere exclusion)), maxmin (MaxMin diversity pick), average (Average linkage (UPGMA)).
  • _subject · object · optionnel
    The record to act on: exactly one of sequence, accession (+source), sample (an id from list_samples) or file ({name, text} or {name, base64}); record_index picks one record of several.
  • clusters · number · optionnel
    average linkage: how many clusters to cut the tree into.
  • molecules · array · requis
    the structures: one SMILES or molfile per entry.
  • threshold · number · optionnel
    Butina: neighbors within this distance (1 − Tanimoto), 0–1.
  • reordering · boolean · optionnel
    Butina: recount unassigned neighbors after each cluster.

  Exemple d'appel

  {"name": "cluster_molecules", "arguments": {"molecules": []}}

  Exemple de retour

  {"content": [{"type": "text", "text": "…"}], "structuredContent": {"picks": "texte", "groups": "texte", "unread": "texte", "summary": "texte"}}

• codon_optimality≈ 809 tokens

  Frequency of optimal codons (Fop, Ikemura 1981) for an in-frame CDS against a real codon-usage table: what share of its codons are the ones a highly-expressed gene in that host would use. Where CAI scores how CLOSE each codon is to its family's best, Fop scores only whether it IS one of the best, which makes it comparable across genes of different amino-acid composition. Name a table this project holds in `table`, or one of the bundled hosts in `host`.

  Paramètres, retour & exemple (6)

  Paramètres

  • host · string · optionnel · E. coli K-12 | H. sapiens | S. cerevisiae
    one of the three codon-usage tables bundled with the app. Only applies when table is not given.
  • table · string · optionnel
    a codon-usage table this project holds, BY NAME, as the Codon Usage panel lists it — any organism. Takes precedence over `host`. This is the way to pass a table you fetched or built; `host` is only the three tables bundled with the app.
  • _files · array · optionnel
    The project: record references shaped like _subject. Their records become library documents a tool names in sequences/parts/document; a trace or alignment is found by file name.
  • _subject · object · optionnel
    The record to act on: exactly one of sequence, accession (+source), sample (an id from list_samples) or file ({name, text} or {name, base64}); record_index picks one record of several.
  • sequence · string · optionnel
    the coding sequence, in frame (a length that is not a multiple of 3 is refused with the reason). Leave it empty to score the open record.
  • threshold · number · optionnel
    Ikemura's optimality cutoff: a codon counts as optimal at this share of its family's most-used codon. 0.8 is the convention, not a measurement, and the right value is host-dependent.

  Exemple d'appel

  {"name": "codon_optimality", "arguments": {"host": "E. coli K-12", "table": "texte", "_files": [], "_subject": {}, "sequence": "texte", "threshold": 1}}

  Exemple de retour

  {"content": [{"type": "text", "text": "…"}], "structuredContent": {"fop": 1, "report": "texte", "scored": 1, "nonOptimal": 1, "optimalCodons": 1}}

• codon_table_fetch≈ 1188 tokens

  Fetch a real codon-usage table for an organism and save it into this project, so later steps can score against it by name. NCBI builds the table by counting codons in the annotated CDS of a RefSeq assembly (the same counting the Codon Usage panel does, with the assembly and CDS count in the provenance); the Kazusa mirror serves a published table for an organism the mirror covers. The table LEAVES NOTHING but takes a network round-trip. Hand the saved name to `codon_usage_analysis` or `codon_optimality` in `table`.

  Paramètres, retour & exemple (7)

  Paramètres

  • mode · string · optionnel · heg | genome
    which CDS set to count. `heg` uses the highly-expressed-gene set, which is what CAI and Fop reference tables are conventionally built from; `genome` counts every annotated CDS, which describes the organism's average gene rather than its best-expressed one. Values: heg (Highly-expressed genes — the CAI/Fop convention), genome (Whole genome — every annotated CDS). Only applies when source is ncbi.
  • _files · array · optionnel
    The project: record references shaped like _subject. Their records become library documents a tool names in sequences/parts/document; a trace or alignment is found by file name.
  • source · string · optionnel · ncbi | kazusa
    which register to build the table from. `ncbi` counts the CDS of a RefSeq assembly and covers any organism with one; `kazusa` serves a published table and covers only the organisms its mirror bundles. Values: ncbi (NCBI RefSeq — counted from annotated CDS, any organism), kazusa (Kazusa/CUTG mirror — published table, bundled organisms only).
  • save_as · string · optionnel
    the name to save the table under, as `table` on the other codon tools will spell it. Defaults to the resolved organism plus the basis, which is what the panel names it.
  • _subject · object · optionnel
    The record to act on: exactly one of sequence, accession (+source), sample (an id from list_samples) or file ({name, text} or {name, base64}); record_index picks one record of several.
  • coverage · string · optionnel · complete | budgeted
    how much of a multi-replicon assembly to download. `complete` takes every replicon; `budgeted` takes the largest ones that fit a memory budget and SAYS which it used. The panel defaults to complete and falls back when the browser cannot hold the whole thing. Values: complete (Complete assembly), budgeted (Budgeted — largest replicons that fit). Only applies when source is ncbi.
  • organism · string · requis
    the organism: a scientific name ("Saccharomyces cerevisiae") or an NCBI taxonomy id ("4932"). Resolved live against NCBI — no allow-list (§1 r4) — and the assembly it picks comes back in `report.builtFrom`.

  Exemple d'appel

  {"name": "codon_table_fetch", "arguments": {"organism": "texte"}}

  Exemple de retour

  {"content": [{"type": "text", "text": "…"}], "structuredContent": {"cds": 1, "gc3": 1, "table": "texte", "codons": 1, "report": "texte", "organism": "texte"}}

• codon_usage_analysis≈ 1600 tokens

  Codon-usage analysis of an in-frame CDS: CAI / expression stats, GC, and every rare-codon occurrence for the chosen organism (pydna port), plus the two bias measures that need NO reference table — ENC (Wright 1990) and RCBS (Roymondal 2009), which are therefore computable for any organism.

  Paramètres, retour & exemple (11)

  Paramètres

  • table · string · optionnel
    score CAI and rare codons against a codon-usage table this project holds, BY NAME, as the Codon Usage panel lists it — any organism, not just the two pydna curates. Takes precedence over `organism`, and switches the rare-codon call from pydna's curated list to `rare_threshold`. Leave unset for the curated pydna report, which is the only arm carrying start/stop weights and the N-end half-life.
  • _files · array · optionnel
    The project: record references shaped like _subject. Their records become library documents a tool names in sequences/parts/document; a trace or alignment is found by file name.
  • feature · string · optionnel
    score this annotated CDS or gene by NAME instead of the selection (the panel's "A CDS / feature…" mode). Its own strand is used unless `reverse` says otherwise.
  • reverse · boolean · optionnel
    read the region as the reverse complement. Leave unset to take the strand from the annotation when the selection is exactly an annotated CDS or gene, which is what the panel does.
  • _subject · object · optionnel
    The record to act on: exactly one of sequence, accession (+source), sample (an id from list_samples) or file ({name, text} or {name, base64}); record_index picks one record of several.
  • organism · string · optionnel · sce | eco
    reference organism for CAI weights + rare codons. Only some organisms carry CAI weights; the rest still get the rare-codon scan + GC.
  • enc_pairs · boolean · optionnel
    count codon PAIRS rather than single codons for ENC (k-mer 2) — bias in the junctions rather than in the codons.
  • rcbs_mean · string · optionnel · geometric | arithmetic
    how the per-codon RCBS weights are averaged. Roymondal 2009 uses the geometric mean. Values: geometric (Geometric (Roymondal 2009)), arithmetic (Arithmetic).
  • rare_threshold · number · optionnel
    a codon is rare when its relative adaptiveness w = f/f_max falls below this. 0.30 is GenScript GenRCA's CFD cutoff, a convention rather than a measurement, so retune it per host. Only applies when table is set.
  • rcbs_directional · boolean · optionnel
    RCBS weights taken as max(observed/expected, expected/observed), so under-use counts as bias too rather than only over-use.
  • enc_bg_correction · boolean · optionnel
    correct ENC for the sequence's own base composition (Novembre 2002). Off is Wright's 1990 ENC, which reads GC-rich genes as more biased than they are.

  Exemple d'appel

  {"name": "codon_usage_analysis", "arguments": {"table": "texte", "_files": [], "feature": "texte", "reverse": true, "_subject": {}, "organism": "sce"}}

  Exemple de retour

  {"content": [{"type": "text", "text": "…"}], "structuredContent": {"gc": 1, "cai": 1, "enc": 1, "rcbs": 1, "codons": 1, "region": "texte", "report": "texte", "codonMap": {}, "rareHits": "texte", "rareBasis": "texte", "caiAvailable": true, "rareFraction": 1}}

• codon_usage_distance≈ 1029 tokens

  How this region's codon usage compares with the record's OTHER genes (CUFS, Diament, Pinter & Tuller 2014). Every other codon score grades one sequence against a reference TABLE; this one grades two sequences against each other, so it stays available for an organism no authority covers. Answers 'does the gene I inserted use codons like the rest of this construct'.

  Paramètres, retour & exemple (5)

  Paramètres

  • _files · array · optionnel
    The project: record references shaped like _subject. Their records become library documents a tool names in sequences/parts/document; a trace or alignment is found by file name.
  • feature · string · optionnel
    score this annotated CDS or gene by NAME instead of the selection (the panel's "A CDS / feature…" mode). Its own strand is used unless `reverse` says otherwise.
  • reverse · boolean · optionnel
    read the region as the reverse complement. Leave unset to take the strand from the annotation when the selection is exactly an annotated CDS or gene, which is what the panel does.
  • _subject · object · optionnel
    The record to act on: exactly one of sequence, accession (+source), sample (an id from list_samples) or file ({name, text} or {name, base64}); record_index picks one record of several.
  • synonymous · boolean · optionnel
    normalise each amino acid's codons to sum to 1 (synCUFS), so what remains is the synonymous choice alone. Off compares all 64 codon frequencies, which also reflects amino-acid composition.

  Exemple d'appel

  {"name": "codon_usage_distance", "arguments": {"_files": [], "feature": "texte", "reverse": true, "_subject": {}, "synonymous": true}}

  Exemple de retour

  {"content": [{"type": "text", "text": "…"}], "structuredContent": {"region": "texte", "ceiling": 1, "nearest": "texte", "skipped": "texte", "compared": 1, "furthest": "texte", "neighbours": "texte", "synonymous": true, "strandSource": "texte", "nearestDistance": 1}}

• compare_antibodies≈ 953 tokens

  Several antibodies side by side: each record numbered by ANARCI, its heavy or its light variable domains aligned column by column by their numbering (a column is one scheme position, so nothing is re-aligned and an insertion is its own column), the CDR of every column under the chosen definition, how many columns agree, and the same properties read off each V domain: length, mass, isoelectric point, net charge, GRAVY, ε280 and the net charge of its CDRs. The alignment is abnumber's `Chain.align`, graded against it over every chain of ANARCI's PDB benchmark; the properties against Biopython ProtParam.

  Paramètres, retour & exemple (7)

  Paramètres

  • pH · number · optionnel
    the pH the net charge and the CDR charge are reported at.
  • chain · string · optionnel · heavy | light
    which variable domains to align: heavy, or light (kappa and lambda together). Values: heavy (Heavy), light (Light (kappa and lambda)).
  • _files · array · optionnel
    The project: record references shaped like _subject. Their records become library documents a tool names in sequences/parts/document; a trace or alignment is found by file name.
  • _subject · object · optionnel
    The record to act on: exactly one of sequence, accession (+source), sample (an id from list_samples) or file ({name, text} or {name, base64}); record_index picks one record of several.
  • antibodies · array · optionnel
    the antibody chains to compare: wire several upstream records here, or list library documents or protein sequences.
  • definition · string · optionnel · imgt | kabat | chothia | north
    the CDR definition, numbered in its own scheme (North in Chothia's). Values: imgt (IMGT), kabat (Kabat), chothia (Chothia), north (North).
  • include_subject · boolean · optionnel
    also compare the open record.

  Exemple d'appel

  {"name": "compare_antibodies", "arguments": {"pH": 1, "chain": "heavy", "_files": [], "_subject": {}, "antibodies": [], "definition": "imgt"}}

  Exemple de retour

  {"content": [{"type": "text", "text": "…"}], "structuredContent": {"rows": "texte", "chains": "texte", "refused": "texte", "regions": "texte", "alignment": "texte", "identical": 1, "mutations": 1, "positions": "texte"}}

• compare_constructions≈ 634 tokens

  Align two constructs' build procedures step by step, in order — was this built the same way as that? Works across formats: a build received as a SnapGene binary and the same build received as an OpenCloning strategy align, because each step's identity is derived from the reaction and its parameters rather than assigned.

  Paramètres, retour & exemple (5)

  Paramètres

  • key · string · optionnel · abstract | processId
    what to align on: `abstract` is the PROCEDURE (the command with its molecules abstracted away, so the same method on different DNA still matches); `processId` is the EXACT recorded operation, identical only when the very same step ran on the very same molecules.
  • _files · array · optionnel
    The project: record references shaped like _subject. Their records become library documents a tool names in sequences/parts/document; a trace or alignment is found by file name.
  • against · string · requis
    File id or name of the construct to compare against, in the same project.
  • _subject · object · optionnel
    The record to act on: exactly one of sequence, accession (+source), sample (an id from list_samples) or file ({name, text} or {name, base64}); record_index picks one record of several.
  • document · string · optionnel
    File id or name for THIS side. The focused document when omitted.

  Exemple d'appel

  {"name": "compare_constructions", "arguments": {"against": "texte"}}

  Exemple de retour

  {"content": [{"type": "text", "text": "…"}], "structuredContent": {"rows": "texte", "shared": 1, "similarity": 1}}

• compare_molecules≈ 784 tokens

  How similar two small molecules are: Tanimoto under six RDKit fingerprints (Morgan/ECFP4, atom pair, topological torsion, RDKit path, pattern, MACCS), every DataStructs metric (Tanimoto, Dice, cosine, Sokal, Russell, Rogot-Goldberg, all-bit, Kulczynski, McConnaughey, asymmetric, Braun-Blanquet, on-bit, Tversky) on the chosen one, and count-based Tanimoto, Dice and Tversky on Morgan counts. The first molecule is the query.

  Paramètres, retour & exemple (7)

  Paramètres

  • other · string · requis
    the structure to compare it with: SMILES or a molfile.
  • _files · array · optionnel
    The project: record references shaped like _subject. Their records become library documents a tool names in sequences/parts/document; a trace or alignment is found by file name.
  • _subject · object · optionnel
    The record to act on: exactly one of sequence, accession (+source), sample (an id from list_samples) or file ({name, text} or {name, base64}); record_index picks one record of several.
  • molecule · string · requis
    the query structure: SMILES or a molfile.
  • tversky_a · number · optionnel
    Tversky's weight on bits only the query has, 0–1.
  • tversky_b · number · optionnel
    Tversky's weight on bits only the other has, 0–1.
  • fingerprint · string · optionnel · morgan | atomPair | torsion | path | pattern | maccs
    the fingerprint every metric is read on. Values: morgan (Morgan (ECFP4)), atomPair (Atom pair), torsion (Topological torsion), path (RDKit path), pattern (Pattern), maccs (MACCS keys).

  Exemple d'appel

  {"name": "compare_molecules", "arguments": {"other": "texte", "molecule": "texte"}}

  Exemple de retour

  {"content": [{"type": "text", "text": "…"}], "structuredContent": {"metrics": "texte", "summary": "texte", "count_similarity": "texte", "tanimoto_by_fingerprint": "texte"}}

• compare_reads_to_reference≈ 1271 tokens

  Compare a SET of sequencing reads against one reference in ONE shared frame: align every read to the reference, vote a consensus column by column, and report the positions where the reads differ from it, each with the change it makes to the protein. This is the whole-plate answer that grading reads one at a time cannot give — a variant is accepted only when every covering read agrees, so a single bad call does not become a mutation. Reads arrive as records or bases; the reference is the record this step runs on.

  Paramètres, retour & exemple (7)

  Paramètres

  • reads · array · optionnel
    the reads to compare — wire a batch of trace RECORDS in (their names come with them, and the per-read table is keyed by name), wire plain sequences, or name project documents.
  • _files · array · optionnel
    The project: record references shaped like _subject. Their records become library documents a tool names in sequences/parts/document; a trace or alignment is found by file name.
  • _subject · object · optionnel
    The record to act on: exactly one of sequence, accession (+source), sample (an id from list_samples) or file ({name, text} or {name, base64}); record_index picks one record of several.
  • end_phred · number · optionnel
    end trimming: the read becomes readable where three consecutive bases reach this score, and everything outside is masked. A Sanger read is unreliable at both ends by construction, which is why the ends are trimmed by RUN rather than per base. Only applies when quality_filter is true.
  • min_phred · number · optionnel
    mask any single base below this phred score. Only applies when quality_filter is true.
  • genetic_code · number · optionnel
    NCBI genetic-code table id, used to say what a variant does to the protein of a CDS on the reference. Advanced.
  • quality_filter · boolean · optionnel
    mask low-quality bases before the vote. Off by default, deliberately: a comparison shows what the FILES say before it shows what a filter says.

  Exemple d'appel

  {"name": "compare_reads_to_reference", "arguments": {"reads": [], "_files": [], "_subject": {}, "end_phred": 1, "min_phred": 1, "genetic_code": 1}}

  Exemple de retour

  {"content": [{"type": "text", "text": "…"}], "structuredContent": {"gaps": "texte", "record": {}, "perRead": "texte", "accepted": 1, "cautions": "texte", "variants": "texte", "consensus": "texte", "conclusion": "texte", "derivation": "texte", "coveragePct": 1, "identityPct": 1}}

• compare_trees≈ 860 tokens

  Compare trees over the same taxa: the Robinson-Foulds distance between two of them, and the consensus of any number. Two methods disagreeing is a result about the data, so the distance and the shared topology are reported together.

  Paramètres, retour & exemple (6)

  Paramètres

  • mode · string · optionnel · majority | strict
    how strict the consensus is: strict keeps only clades in EVERY tree; majority keeps those above the cutoff. Values: majority (Majority-rule), strict (Strict).
  • trees · array · requis
    two or more trees in Newick (NEXUS, PhyloXML and NeXML pastes are sniffed too) — wire `newick` outputs here.
  • _files · array · optionnel
    The project: record references shaped like _subject. Their records become library documents a tool names in sequences/parts/document; a trace or alignment is found by file name.
  • cutoff · number · optionnel
    the fraction of trees a clade must appear in for a majority consensus. Only applies when mode is majority.
  • _subject · object · optionnel
    The record to act on: exactly one of sequence, accession (+source), sample (an id from list_samples) or file ({name, text} or {name, base64}); record_index picks one record of several.
  • sharedTaxaOnly · boolean · optionnel
    prune every tree to the taxa they ALL share before comparing, instead of refusing a mismatch. The numbers then describe the pruned trees, and pruning can only remove or merge splits, so the distance is a lower bound on the disagreement between the trees as given.

  Exemple d'appel

  {"name": "compare_trees", "arguments": {"trees": []}}

  Exemple de retour

  {"content": [{"type": "text", "text": "…"}], "structuredContent": {"rf": 1, "consensus": "texte", "distances": "texte", "treeCount": 1, "normalized": 1, "prunedTaxa": "texte", "comparedTaxa": 1}}

• consensus_from_traces≈ 1318 tokens

  Merge one or two Sanger reads into a consensus with the ported SeqTrace caller. With two reads (typically a forward and a reverse of the same amplicon) an IUPAC ambiguity code marks a position the two DISAGREE about; with one read there is nothing to disagree with and a code marks a position where no single base cleared the confidence bar. Returns the consensus, how many positions are ambiguous, and how many the consensus's own trimming stage cut from the ends.

  Paramètres, retour & exemple (15)

  Paramètres

  • _files · array · optionnel
    The project: record references shaped like _subject. Their records become library documents a tool names in sequences/parts/document; a trace or alignment is found by file name.
  • _subject · object · optionnel
    The record to act on: exactly one of sequence, accession (+source), sample (an id from list_samples) or file ({name, text} or {name, base64}); record_index picks one record of several.
  • document · string · optionnel
    the first read: its name or its project file id.
  • min_conf · number · optionnel
    the confidence a base must clear to be called rather than written as a code. SeqTrace range 1-61.
  • algorithm · string · optionnel · Bayesian | legacy
    Bayesian converts each base's Phred to a posterior and combines the reads position by position; legacy lets the higher-confidence base win each position outright. They are different callers, not settings of one.
  • trim_window · number · optionnel
    how many consensus bases the quality-trim mean is taken over. Wider is more forgiving of a single bad base and slower to stop at a genuinely bad end. Advanced.
  • primer_match · number · optionnel
    the fraction of a primer that must match for it to be cut. 1 is exact; lower tolerates the mismatches a real read carries at its noisy start. Only applies when trim_primers is true. Advanced.
  • quality_trim · boolean · optionnel
    trim the consensus's own ends by quality. Note this is the stage primer trimming lives inside, so primer trimming does nothing without it.
  • trim_primers · boolean · optionnel
    cut the primers off the consensus ends. It runs INSIDE the quality-trim stage, so turning it on turns that stage on too.
  • trim_end_gaps · boolean · optionnel
    also cut the gap runs at each end, where only one read reached. With two reads those stretches are single-read consensus and read as agreement when they are not. Advanced.
  • trim_min_good · number · optionnel
    how many of those bases must clear `min_conf` for the window to be kept. It cannot exceed `trim_window` and is clamped to it rather than refused. Advanced.
  • forward_primer · string · optionnel
    the forward primer to cut, 5→3. Only applies when trim_primers is true.
  • reverse_primer · string · optionnel
    the reverse primer to cut, 5→3. Only applies when trim_primers is true.
  • second_document · string · optionnel
    the second read, usually the reverse of the same amplicon. Leave empty for a single-read consensus, which is a different question and is reported as one.
  • reverse_complement_second · boolean · optionnel
    reverse-complement the second read before merging. A reverse read of the same amplicon needs this; two forward reads do not.

  Exemple d'appel

  {"name": "consensus_from_traces", "arguments": {"_files": [], "_subject": {}, "document": "texte", "min_conf": 1, "algorithm": "Bayesian", "trim_window": 1}}

  Exemple de retour

  {"content": [{"type": "text", "text": "…"}], "structuredContent": {"length": 1, "reading": "texte", "consensus": "texte", "readsUsed": 1, "trimmedFromEnds": 1, "ambiguousPositions": 1}}

• copy_number_allele_split≈ 894 tokens

  Read an Affymetrix array result's own allele-specific copy number: for each segment the major and minor allele counts (1+1, 2+0, 0+0), what they mean (balanced, allelic imbalance, loss of heterozygosity placed against the sample's own ploidy, homozygous deletion), and ASCAT's whole-genome summary over them (LOH fraction, homozygous deletions, modal allele state, whole-genome doubling, genomic instability). OncoScan results state a split when the aberrant-cell fraction was determined; the tool says why when a file states none.

  Paramètres, retour & exemple (4)

  Paramètres

  • file · string · optionnel
    which copy-number file in this project, by name. Unset, it is the project's only one, and it refuses rather than guessing when there are several.
  • _files · array · optionnel
    The project: record references shaped like _subject. Their records become library documents a tool names in sequences/parts/document; a trace or alignment is found by file name.
  • _subject · object · optionnel
    The record to act on: exactly one of sequence, accession (+source), sample (an id from list_samples) or file ({name, text} or {name, base64}); record_index picks one record of several.
  • estimated_only · boolean · optionnel
    report only the segments the producer split. Default false: an unestimated segment is listed as such, which is a different answer from its absence.

  Exemple d'appel

  {"name": "copy_number_allele_split", "arguments": {"file": "texte", "_files": [], "_subject": {}, "estimated_only": true}}

  Exemple de retour

  {"content": [{"type": "text", "text": "…"}], "structuredContent": {"metrics": "texte", "summary": "texte", "segments": "texte", "provenance": "texte"}}

• copy_number_compare≈ 1353 tokens

  Join two Affymetrix copy-number samples' own calls and report which events they share and which only one of them carries: for every pair, the chromosome both files resolved to, the kind, the bases they overlap and their reciprocal overlap; and separately each sample's unshared calls. Kind is part of the match, so a gain in one sample and a loss in the other at one locus are reported as two unshared calls rather than as agreement. Chromosomes only one file indexes are listed apart and are NOT reported as differences: nothing about them was compared. NO OVERLAP THRESHOLD IS APPLIED — every pair comes back with its numbers, and which agreement counts as agreement is a laboratory's judgement.

  Paramètres, retour & exemple (8)

  Paramètres

  • file · string · optionnel
    which copy-number file in this project is the first sample, by name. Unset, it is the project's only one — and it refuses rather than guessing when there is more than one.
  • _files · array · optionnel
    The project: record references shaped like _subject. Their records become library documents a tool names in sequences/parts/document; a trace or alignment is found by file name.
  • compare · string · requis
    which copy-number file in this project is the second sample, by name — the same parameter copy_number_read.compare takes. Required: there is no default second sample, and a file compared with itself answers one question twice.
  • _subject · object · optionnel
    The record to act on: exactly one of sequence, accession (+source), sample (an id from list_samples) or file ({name, text} or {name, base64}); record_index picks one record of several.
  • data_set · string · optionnel
    which data set of the first file to scan, by name. Unset is the file's FIRST, which is what the panel opens on.
  • min_bases · number · optionnel
    ignore any call spanning fewer bases than this, on BOTH sides. Default 0, for the same reason as min_markers. Note a single-marker call spans 0 bases.
  • min_markers · number · optionnel
    ignore any call shorter than this many markers, on BOTH sides. The default counts everything either file called, because a reporting floor belongs to the laboratory and not to this tool — and it is the same floor copy_number_findings applies.
  • compare_data_set · string · optionnel
    which data set of the second file to scan. Unset is that file's FIRST.

  Exemple d'appel

  {"name": "copy_number_compare", "arguments": {"compare": "texte"}}

  Exemple de retour

  {"content": [{"type": "text", "text": "…"}], "structuredContent": {"shared": "texte", "summary": "texte", "compared": "texte", "provenance": "texte", "only_in_file": "texte", "only_in_compare": "texte", "unmatched_chromosomes": "texte"}}

• copy_number_findings≈ 1084 tokens

  Scan every indexed chromosome of an Affymetrix copy-number container and report what the file itself called: gains, losses and stretches of homozygosity, with their positions, marker counts and spans, plus a per-chromosome summary. Reads the file's own CNState and LOH columns and infers nothing — for a second opinion computed from the log2 ratios, use copy_number_segment. A chromosome that was read and carries nothing is reported as clean, which is a different answer from one that could not be read. NO GENOME BUILD IS ASSUMED: positions are the file's own.

  Paramètres, retour & exemple (6)

  Paramètres

  • file · string · optionnel
    which copy-number file in this project, by name. Unset, it is the project's only one — and it refuses rather than guessing when there is more than one.
  • _files · array · optionnel
    The project: record references shaped like _subject. Their records become library documents a tool names in sequences/parts/document; a trace or alignment is found by file name.
  • _subject · object · optionnel
    The record to act on: exactly one of sequence, accession (+source), sample (an id from list_samples) or file ({name, text} or {name, base64}); record_index picks one record of several.
  • data_set · string · optionnel
    which data set to scan, by name. Unset is the file's FIRST, which is what the panel opens on.
  • min_bases · number · optionnel
    ignore any run spanning fewer bases than this. Default 0, for the same reason as min_markers. Note a single-marker run spans 0 bases.
  • min_markers · number · optionnel
    ignore any run shorter than this many markers. The default counts everything the file called, including single markers, because a reporting floor belongs to the laboratory and not to this tool.

  Exemple d'appel

  {"name": "copy_number_findings", "arguments": {"file": "texte", "_files": [], "_subject": {}, "data_set": "texte", "min_bases": 1, "min_markers": 1}}

  Exemple de retour

  {"content": [{"type": "text", "text": "…"}], "structuredContent": {"bed": "texte", "source": "texte", "summary": "texte", "findings": "texte", "chromosomes": "texte"}}

• copy_number_loh≈ 1053 tokens

  Recompute loss of heterozygosity from an Affymetrix array's own per-marker genotype calls, rather than reading the runs the producer wrote: APT's window method, with the false-positive rate and the assumed genotyping error rate as parameters. Answers where a sample has lost one parental haplotype, including where copy number is normal. Needs a container that states genotype calls — an OncoScan OSCHP does; a CytoScan CYCHP states the set with no rows, and this says so rather than answering empty.

  Paramètres, retour & exemple (6)

  Paramètres

  • file · string · optionnel
    which copy-number file in this project, by name. Unset, it is the project's only one — and it refuses rather than guessing when there are several.
  • alpha · number · optionnel
    APT's `lohCN_alpha`: the false-positive rate the heterozygote cutoff is set against. Raising it makes the window narrower and the method readier to call a run, which is the knob to move when comparing against another caller.
  • _files · array · optionnel
    The project: record references shaped like _subject. Their records become library documents a tool names in sequences/parts/document; a trace or alignment is found by file name.
  • _subject · object · optionnel
    The record to act on: exactly one of sequence, accession (+source), sample (an id from list_samples) or file ({name, text} or {name, base64}); record_index picks one record of several.
  • error_rate · number · optionnel
    APT's `lohCN_errorrate`: the assumed genotyping error rate, which is what makes a heterozygote inside a homozygous stretch explicable. It is RE-ESTIMATED from the sample's own no-call rate when the genotype confidences reach the no-call threshold, and the output says which value was actually used.
  • min_genomic_span · number · optionnel
    APT's `lohCN_minGenomicSpan`: a called run narrower than this many base pairs is dropped. The default is the vendor's 1,000,000.

  Exemple d'appel

  {"name": "copy_number_loh", "arguments": {"file": "texte", "alpha": 1, "_files": [], "_subject": {}, "error_rate": 1, "min_genomic_span": 1}}

  Exemple de retour

  {"content": [{"type": "text", "text": "…"}], "structuredContent": {"runs": "texte", "window": "texte", "summary": "texte", "accounting": "texte", "provenance": "texte"}}

• copy_number_mosaicism≈ 1190 tokens

  Estimate which mosaic fraction class each region of one chromosome is closest to, as Affymetrix Power Tools computes it. A mosaic event is present in only some of the sample's cells, so its log2 ratio sits between the levels a clonal change would produce. Every segment comes back with the class it was assigned (±0.3, ±0.5, ±0.7, ±1.0), the fraction that class is NAMED for, its confidence, and whether the method CALLED it as mosaic — a whole-copy change of exactly ±1.0 is clonal and is reported with call 0, which is the vendor's own test. The mixture values are class labels, not measured cell fractions: there is no published method for this estimate and no independent implementation to grade it against, so it is reported as APT computes it and the provenance output carries that sentence. A chromosome with fewer than 4,330 markers is refused by name rather than answered empty, because the method's own boundary adjustments would delete every call.

  Paramètres, retour & exemple (8)

  Paramètres

  • file · string · optionnel
    which copy-number file in this project, by name. Unset, it is the project's only one — and it refuses rather than guessing when there is more than one.
  • graph · string · optionnel
    which graph column to read. Unset is the first log2-ratio column, the same rule copy_number_segment applies. A column that is not a log2 ratio is refused rather than smoothed: a copy-number STATE column is already someone's answer.
  • _files · array · optionnel
    The project: record references shaped like _subject. Their records become library documents a tool names in sequences/parts/document; a trace or alignment is found by file name.
  • _subject · object · optionnel
    The record to act on: exactly one of sequence, accession (+source), sample (an id from list_samples) or file ({name, text} or {name, base64}); record_index picks one record of several.
  • data_set · string · optionnel
    which data set to read, by name. Unset is the file's FIRST, which is what the panel opens on.
  • chromosome · number · optionnel
    which chromosome, as the file numbers them (1-22, then 23=X, 24=Y, 25=MT — the file's own convention). Unset is the first the index carries. A chromosome too short for the method is refused with the count it has and the ones that would run.
  • mosaic_bandwidth · number · optionnel
    the smoothing window in markers — APT's own `marker-bandwidth`. A mosaic event is a shallow wide elevation, so this is what decides how wide 'wide' is. The default is the vendor's shipped value.
  • mosaic_confidence_window · number · optionnel
    the running-median window used to score a segment, in markers — APT's own `confidence-window`. The default is the vendor's shipped value.

  Exemple d'appel

  {"name": "copy_number_mosaicism", "arguments": {"file": "texte", "graph": "texte", "_files": [], "_subject": {}, "data_set": "texte", "chromosome": 1}}

  Exemple de retour

  {"content": [{"type": "text", "text": "…"}], "structuredContent": {"called": "texte", "summary": "texte", "segments": "texte", "provenance": "texte"}}

• copy_number_read≈ 1468 tokens

  Read an Affymetrix copy-number container (CNCHP/CYCHP/OSCHP/CHP) in this project and say what is in it: the algorithm and array that produced it, its data sets and their graphs, the per-chromosome marker index the file carries, and — for one chromosome — each graph decimated to a summary with its real range. Values the analysis left undefined are counted and reported, never plotted as zero. NO GENOME BUILD IS ASSUMED: positions are the file's own, because these files name an annotation release and not an assembly.

  Paramètres, retour & exemple (9)

  Paramètres

  • end · number · optionnel
    last base of the region to summarize. Unset is the chromosome's last marker. Given with `start`, the graphs are decimated over that window instead of the whole chromosome: the same thing the panel's Region field does.
  • bins · number · optionnel
    how many buckets to decimate each graph into. The panel uses one per pixel column of its plot; a smaller number here is a coarser summary of the same data.
  • file · string · optionnel
    which copy-number file in this project, by name. Unset, it is the project's only one — and it refuses rather than guessing when there is more than one.
  • start · number · optionnel
    first base of the region to summarize, on the selected chromosome. Unset is the chromosome's first marker. Clamped to what the file's markers actually cover, because a locus is a position in the assembly and an array's coverage stops where it stops.
  • _files · array · optionnel
    The project: record references shaped like _subject. Their records become library documents a tool names in sequences/parts/document; a trace or alignment is found by file name.
  • compare · string · optionnel
    a SECOND copy-number file in this project, by name, to read over the SAME chromosome, the same window and the same buckets — the overlay the canvas draws, as numbers. Its chromosome is matched by LABEL and not by number, because each file states its own numbering, and its graphs are matched by COLUMN NAME, so a file carrying a different set of them reports which it has rather than answering from whatever sits at that position. Unset, nothing of a second file is read.
  • _subject · object · optionnel
    The record to act on: exactly one of sequence, accession (+source), sample (an id from list_samples) or file ({name, text} or {name, base64}); record_index picks one record of several.
  • data_set · string · optionnel
    which data set to read, by name. Unset is the file's FIRST, which is what the panel opens on.
  • chromosome · number · optionnel
    which chromosome's markers to summarize, as THE FILE numbers them. The autosomes are 1-22; which numbers are X and Y is stated by the file's own header (`xChromosome`/`yChromosome`, which both bundled arrays give as 24 and 25) and read from it rather than assumed. Unset is the first the index carries, which is what the panel selects.

  Exemple d'appel

  {"name": "copy_number_read", "arguments": {"end": 1, "bins": 1, "file": "texte", "start": 1, "_files": [], "compare": "texte"}}

  Exemple de retour

  {"content": [{"type": "text", "text": "…"}], "structuredContent": {"tracks": "texte", "summary": "texte", "compared": "texte", "data_sets": "texte", "provenance": "texte", "chromosomes": "texte", "index_source": "texte"}}

• copy_number_regions≈ 1354 tokens

  Place an Affymetrix copy-number sample's own calls in ClinGen's curated regions: for each region, which gains, losses or stretches of homozygosity fall in it, at what reciprocal overlap, and how much of the region they cover between them. Regions come from ClinGen's dosage-sensitivity curation, cached with its retrieval date — a loss is reported against the region's haploinsufficiency score and a gain against its triplosensitivity score, and no score is claimed for LOH or mosaic events, which change no copy number. NO THRESHOLD IS APPLIED: every overlap is reported with its numbers and which calls are worth reporting is a laboratory's judgement. Regions ClinGen has not placed on this build are listed separately and are NOT reported as clean.

  Paramètres, retour & exemple (8)

  Paramètres

  • file · string · optionnel
    which copy-number file in this project, by name. Unset, it is the project's only one — and it refuses rather than guessing when there is more than one.
  • build · string · optionnel · hg19 | hg38
    which assembly's curated region list to place the calls on. Unset is the build THIS FILE states about itself, and the node refuses rather than guessing when it states none — a region is a pair of coordinates, and placing a call on the wrong assembly moves every boundary by hundreds of kilobases with nothing to show it. Values: hg19 (hg19 / GRCh37), hg38 (hg38 / GRCh38).
  • _files · array · optionnel
    The project: record references shaped like _subject. Their records become library documents a tool names in sequences/parts/document; a trace or alignment is found by file name.
  • regions · string · optionnel
    a BED region file in this project, by name, to check against INSTEAD of ClinGen's curated list — the laboratory's own panel, which is what ChAS calls the CytoRegion file. Unset is ClinGen. A BED line states no dosage score, so with this set every hit comes back with dosage null: the list says where to look and claims nothing about what a change there means. If the file states an assembly on its track line (`track ... db=hg19`) and it is not the build being read, the node refuses rather than moving every boundary by hundreds of kilobases.
  • _subject · object · optionnel
    The record to act on: exactly one of sequence, accession (+source), sample (an id from list_samples) or file ({name, text} or {name, base64}); record_index picks one record of several.
  • data_set · string · optionnel
    which data set to scan, by name. Unset is the file's FIRST, which is what the panel opens on.
  • min_bases · number · optionnel
    ignore any call spanning fewer bases than this. Default 0, for the same reason as min_markers. Note a single-marker call spans 0 bases.
  • min_markers · number · optionnel
    ignore any call shorter than this many markers. The default counts everything the file called, because a reporting floor belongs to the laboratory and not to this tool — and it is the same floor copy_number_findings applies, so both doors place the same calls.

  Exemple d'appel

  {"name": "copy_number_regions", "arguments": {"file": "texte", "build": "hg19", "_files": [], "regions": "texte", "_subject": {}, "data_set": "texte"}}

  Exemple de retour

  {"content": [{"type": "text", "text": "…"}], "structuredContent": {"regions": "texte", "summary": "texte", "unplaced": "texte", "provenance": "texte"}}

• copy_number_segment≈ 2481 tokens

  Segment one chromosome of an Affymetrix copy-number container by up to four independent methods and report where they agree. The HMM lays a copy-number model over the log2 ratios and calls a state per segment; circular binary segmentation finds where the mean changes with no model of what a gain looks like, by permutation test; piecewise constant fitting picks the piecewise-constant curve minimizing squared error plus a penalty per jump, with no test and no seed; PELT minimizes the same shape of objective exactly and prices a boundary with an information criterion rather than a tuned constant, so its segment count follows from a model-selection rule. Every parameter and every default is the canvas's own. NO GENOME BUILD IS ASSUMED and no method is on unless asked for.

  Paramètres, retour & exemple (22)

  Paramètres

  • file · string · optionnel
    which copy-number file in this project, by name. Unset, it is the project's only one — and it refuses rather than guessing when there is more than one.
  • graph · string · optionnel
    which graph column to segment. Unset is the first log2-ratio column, which is what the panel segments. A column that is not a log2 ratio is refused rather than segmented: a copy-number STATE column is already someone's answer.
  • _files · array · optionnel
    The project: record references shaped like _subject. Their records become library documents a tool names in sequences/parts/document; a trace or alignment is found by file name.
  • cbs_eta · number · optionnel
    DNAcopy's `eta`: the error budget for stopping each permutation test early once its outcome is settled. Not the significance level; any value but 0.05 recomputes the stopping boundary. Same default as the panel.
  • methods · string · optionnel
    which methods to run, comma-separated: `hmm`, `cbs`, `pcf`, `pelt`. Unset runs all four, because the point of this node is where they agree. The panel has each of them off until asked, so running one here is not a different default — it is the same control, pressed.
  • _subject · object · optionnel
    The record to act on: exactly one of sequence, accession (+source), sample (an id from list_samples) or file ({name, text} or {name, base64}); record_index picks one record of several.
  • cbs_seed · number · optionnel
    CBS accepts a boundary by permutation test, so the run is seeded and about 1 borderline dataset in 40 segments differently under a different seed. Same default as the panel.
  • cbs_trim · number · optionnel
    DNAcopy's `trim`: the fraction cut from each tail before sdundo measures the noise SD. Read only when `cbs_undo_splits` is sdundo. Same default as the panel. Only applies when cbs_undo_splits is sdundo.
  • data_set · string · optionnel
    which data set to segment, by name. Unset is the file's FIRST, which is what the panel opens on.
  • pcf_kmin · number · optionnel
    PCF's shortest allowed segment, in markers — the finest change the fit may claim. Same default as the panel.
  • hmm_model · string · optionnel · file | apt-cn-state | apt-cn-cyto2
    which copy-number state model the HMM calls against. `file` is the model the container's own header states, and is used when unset if the file states one; otherwise the first preset. `apt-cn-state` is APT's generic method with its GC-corrected means, `apt-cn-cyto2` the six-state method written for CytoScan arrays. The panel lists the same models in the same order. Values: file (This file’s own parameters), apt-cn-state (APT cn-state (GC-corrected)), apt-cn-cyto2 (APT cn-cyto2 (CytoScan)).
  • pcf_gamma · number · optionnel
    PCF's penalty per jump — how much evidence a level change must carry. Scaled by the squared MAD noise estimate unless `pcf_normalize` is off, which is what makes 40 mean the same thing on a quiet array and a noisy one. Same default as the panel.
  • chromosome · number · optionnel
    which chromosome to segment, as the file numbers them (1-22, then 23=X, 24=Y, 25=MT — the file's own convention). Unset is the first the index carries, which is what the panel selects.
  • pcf_method · string · optionnel · auto | exact | fast
    which piecewise-constant fit: `auto` (copynumber's own rule — the exact dynamic program under 400 markers, its selectFastPcf approximation above), `exact`, or `fast`. Both are ported and graded against R, so this is a real choice. `exact` is refused above 25,000 markers rather than silently downgraded: it is quadratic there (21 s at 100,000), where the approximation fits a whole 142,000-marker chromosome in about 0.3 s. Same default as the panel. Values: auto (Automatic), exact (Exact), fast (Approximate).
  • cbs_undo_sd · number · optionnel
    DNAcopy's `undo.SD`: the merge threshold in trimmed noise SDs. Read only when `cbs_undo_splits` is sdundo. Same default as the panel. Only applies when cbs_undo_splits is sdundo.
  • pelt_penalty · string · optionnel · MBIC | BIC | SIC0 | AIC | Hannan-Quinn | Manual | None
    PELT's penalty, and the reason its knob is a different KIND of knob from PCF's gamma: it is an information criterion, so the number of segments follows from a model-selection rule rather than from a constant calibrated against this array's noise. MBIC is changepoint's own default and adds log(segment length) to each segment's cost as well as its (parameters + 2)·log(n) penalty. `Manual` is the only one that reads `pelt_penalty_value`. Same default as the panel. Values: MBIC (MBIC), BIC (BIC), SIC0 (BIC without the location term), AIC (AIC), Hannan-Quinn (Hannan-Quinn), Manual (Manual), None (None).
  • pcf_normalize · boolean · optionnel
    scale the PCF penalty by the squared MAD noise estimate (the vendor’s `normalize`). Off makes gamma an absolute penalty in squared log2 units, which is a different parameter wearing the same name. Same default as the panel.
  • cbs_undo_prune · number · optionnel
    DNAcopy's `undo.prune`: the fractional increase in residual cost pruning may accept. Read only when `cbs_undo_splits` is prune. Same default as the panel. Only applies when cbs_undo_splits is prune.
  • pelt_minseglen · number · optionnel
    PELT's shortest allowed segment, in markers (changepoint's `minseglen`) — the finest change the fit may claim. Same default as the panel.
  • cbs_undo_splits · string · optionnel · none | sdundo | prune
    DNAcopy's `undo.splits`, the post-hoc merge over what CBS found: `none` keeps every significant split, `sdundo` merges adjacent segments whose medians are within `cbs_undo_sd` trimmed SDs (is this boundary bigger than the noise?), `prune` keeps the fewest change points whose cost stays within `cbs_undo_prune` (how few boundaries explain this almost as well?). Same default as the panel. Values: none (Keep every split), sdundo (Merge within SDs), prune (Prune by cost).
  • pelt_standardize · boolean · optionnel
    divide by the robust MAD before fitting. ON by default, and this is the one PELT default that is ours rather than the vendor's, because the vendor documents the assumption and does not enforce it: a change-in-mean cost is a raw residual sum of squares while the penalty is on a log(n) scale, so the two are only commensurate at unit variance. Off, a noisy array buys boundaries it should not and a quiet one buys none, and both look like plausible answers. Same default as the panel.
  • pelt_penalty_value · number · optionnel
    the cost a boundary must save to be worth buying, in the cost function's own units. Read ONLY when `pelt_penalty` is Manual; the named criteria derive their own from the marker count. Same default as the panel. Only applies when pelt_penalty is Manual.

  Exemple d'appel

  {"name": "copy_number_segment", "arguments": {"file": "texte", "graph": "texte", "_files": [], "cbs_eta": 1, "methods": "texte", "_subject": {}}}

  Exemple de retour

  {"content": [{"type": "text", "text": "…"}], "structuredContent": {"summary": "texte", "segments": "texte", "agreement": "texte", "derivation": "texte"}}

• copy_number_somatic≈ 902 tokens

  Read an Affymetrix array result's own somatic-mutation calls: one row per mutation probe set with the producer's call, the score behind it and the two thresholds that call was graded against. OncoScan CNV Plus states this table; CytoScan and SNP 6.0 results do not, and the tool says so rather than answering empty.

  Paramètres, retour & exemple (4)

  Paramètres

  • file · string · optionnel
    which copy-number file in this project, by name. Unset, it is the project's only one — and it refuses rather than guessing when there are several.
  • _files · array · optionnel
    The project: record references shaped like _subject. Their records become library documents a tool names in sequences/parts/document; a trace or alignment is found by file name.
  • _subject · object · optionnel
    The record to act on: exactly one of sequence, accession (+source), sample (an id from list_samples) or file ({name, text} or {name, base64}); record_index picks one record of several.
  • detected_only · boolean · optionnel
    report only the calls the producer detected. Default false: the undetected rows are what say the probe set was READ and came back wild type, which is a different answer from the probe set being absent.

  Exemple d'appel

  {"name": "copy_number_somatic", "arguments": {"file": "texte", "_files": [], "_subject": {}, "detected_only": true}}

  Exemple de retour

  {"content": [{"type": "text", "text": "…"}], "structuredContent": {"calls": "texte", "summary": "texte", "detected": "texte", "provenance": "texte"}}

• crispr_analyze_screen≈ 1234 tokens

  Call HITS from a pooled CRISPR screen: per-guide read counts in, a gene-level Bayes factor and a precision/recall curve out. This is the other end of a screen from the pool designer — it reads what came back rather than deciding what to order. The estimator is BAGEL2 (Kim & Hart 2021), reproduced byte-for-byte against upstream, so a gene's Bayes factor here is the number BAGEL2 prints for the same counts. It is a COMPARISON against two reference gene sets, not an absolute fitness measure, and it reports how many of those reference genes the library actually carries, because a screen whose gene symbols do not match the reference sets trains on almost nothing and still returns a ranking. MAGeCK's alpha-RRA and drugZ are different statistics that disagree with this one on the same counts; neither is computed here, and a hit list must say which statistic produced it.

  Paramètres, retour & exemple (11)

  Paramètres

  • _files · array · optionnel
    The project: record references shaped like _subject. Their records become library documents a tool names in sequences/parts/document; a trace or alignment is found by file name.
  • fdr_cut · number · optionnel
    the false-discovery rate the hit list is cut at. A DISPLAY threshold read off the computed curve, not a parameter of the estimator.
  • _subject · object · optionnel
    The record to act on: exactly one of sequence, accession (+source), sample (an id from list_samples) or file ({name, text} or {name, base64}); record_index picks one record of several.
  • min_reads · number · optionnel
    drop a reagent whose SUMMED control count is below this (upstream's -m). Applied after the pseudocount, exactly as upstream applies it.
  • read_counts · string · requis
    the count table: a header line, then one row per reagent — identifier, gene, then one column per sequenced sample. Tab- or comma-separated. Counts may be written as decimals, as upstream's own files are.
  • pseudo_count · number · optionnel
    added to every count before normalising to 10,000,000 reads per column. Advanced.
  • sample_columns · array · optionnel
    which sample column names to score. Leave empty to score every column that is not a control.
  • control_columns · array · requis
    the T0 / plasmid column NAMES, exactly as the header spells them. Summed before the fold change, so a two-replicate T0 is one control and not two.
  • essential_genes · string · requis
    reference ESSENTIAL gene symbols, one per line (extra columns ignored). BAGEL2's CEGv2 is the usual choice; the editor panel ships it and the mouse set beside it.
  • equalise_replicates · number · optionnel
    scale every Bayes factor as if the screen had this many replicates (upstream's -p), 0 to leave it off. A BF is a SUM over replicates, so two screens of different replicate counts are not comparable until this is set. Advanced.
  • non_essential_genes · string · requis
    reference NON-ESSENTIAL gene symbols, one per line. BAGEL2's NEGv1 is the usual choice.

  Exemple d'appel

  {"name": "crispr_analyze_screen", "arguments": {"read_counts": "texte", "control_columns": [], "essential_genes": "texte", "non_essential_genes": "texte"}}

  Exemple de retour

  {"content": [{"type": "text", "text": "…"}], "structuredContent": {"fit": "texte", "hits": 1, "curve": "texte", "genes": "texte", "hitBf": 1, "training": "texte"}}

• crispr_design_guides≈ 737 tokens

  Design and score CRISPR guides on the subject — on/off-target scores, QC flags, and cloning-enzyme conflicts. Nuclease list comes from the real nuclease registry.

  Paramètres, retour & exemple (7)

  Paramètres

  • _files · array · optionnel
    The project: record references shaped like _subject. Their records become library documents a tool names in sequences/parts/document; a trace or alignment is found by file name.
  • _subject · object · optionnel
    The record to act on: exactly one of sequence, accession (+source), sample (an id from list_samples) or file ({name, text} or {name, base64}); record_index picks one record of several.
  • min_stem · number · optionnel
    minimum self-complementary stem to report. In nt. Advanced.
  • nuclease · string · optionnel · SpCas9 | SpCas9-NG | SpG | SpRY | xCas9 | SaCas9 | SaCas9-KKH | AsCas12a
    the nuclease (PAM + spacer length) to scan for. Values: SpCas9 (SpCas9: NGG (3')), SpCas9-NG (SpCas9-NG: NG (3')), SpG (SpG: NGN (3')), SpRY (SpRY: NRN (3')), xCas9 (xCas9: NG (3')), SaCas9 (SaCas9: NNGRRT (3')), SaCas9-KKH (SaCas9-KKH: NNNRRT (3')), AsCas12a (AsCas12a: TTTV (5')), LbCas12a (LbCas12a: TTTV (5')), enAsCas12a (enAsCas12a: TTTV (5')).
  • region_end · number · optionnel
    restrict results to guides ending at/before this position. In bp. Advanced.
  • region_start · number · optionnel
    restrict results to guides starting at/after this position (0-based). In bp. Advanced.
  • restriction_enzymes · array · optionnel
    cloning enzymes whose recognition site must NOT appear in the spacer. Advanced.

  Exemple d'appel

  {"name": "crispr_design_guides", "arguments": {"_files": [], "_subject": {}, "min_stem": 1, "nuclease": "SpCas9", "region_end": 1, "region_start": 1}}

  Exemple de retour

  {"content": [{"type": "text", "text": "…"}], "structuredContent": {"count": 1, "guides": "texte", "topSpacer": "texte", "totalCandidates": 1}}

• crispr_design_library≈ 1587 tokens

  Turn the open record's annotated targets into an ORDERABLE sgRNA oligo pool: the best N guides per target, filtered at order time (Pol-III terminator, Graf inactive motif, cloning-enzyme site, minimum on-target score), each composed into the oligo a synthesiser makes — the vector's cloning overhangs around the spacer plus, optionally, one of CRISPOR's eleven subpool barcodes. A spacer that serves two overlapping targets takes ONE well, and every candidate a filter held back is counted by reason, so a short pool says which rule shortened it. It designs a library; it does not analyse one. No recommended representation, MOI or read depth is embedded — the screen-scale arithmetic is in the editor panel, where the numbers are the user's.

  Paramètres, retour & exemple (16)

  Paramètres

  • moi · number · optionnel
    multiplicity of infection, 0 to leave it unplanned. Joung et al. 2017 recommends <0.3 so most cells take at most one perturbation; reported, never applied. Advanced.
  • rank · string · optionnel · ruleSet1 | crisprScan | crisprRater
    which on-target score orders the candidates. A guide the chosen model cannot score is left unranked, never dropped. Rule Set 3 is deliberately not offered here: its weights are a 9.8 MB download the editor fetches on demand, and this engine is headless and cannot fetch — offering it would return an unranked pool that looked ranked.
  • _files · array · optionnel
    The project: record references shaped like _subject. Their records become library documents a tool names in sequences/parts/document; a trace or alignment is found by file name.
  • _subject · object · optionnel
    The record to act on: exactly one of sequence, accession (+source), sample (an id from list_samples) or file ({name, text} or {name, base64}); record_index picks one record of several.
  • nuclease · string · optionnel · SpCas9 | SpCas9-NG | SpG | SpRY | xCas9 | SaCas9 | SaCas9-KKH | AsCas12a
    the nuclease (PAM + spacer length) to scan for. Values: SpCas9 (SpCas9: NGG (3')), SpCas9-NG (SpCas9-NG: NG (3')), SpG (SpG: NGN (3')), SpRY (SpRY: NRN (3')), xCas9 (xCas9: NG (3')), SaCas9 (SaCas9: NNGRRT (3')), SaCas9-KKH (SaCas9-KKH: NNNRRT (3')), AsCas12a (AsCas12a: TTTV (5')), LbCas12a (LbCas12a: TTTV (5')), enAsCas12a (enAsCas12a: TTTV (5')).
  • barcode_id · number · optionnel
    CRISPOR subpool barcode id, 0 for none — lets several sub-libraries share one synthesis array and amplify apart. Advanced.
  • target_type · string · optionnel
    annotation type to take as the targets, one pool entry per feature of that type (`CDS`, `gene`, …). Leave unset to treat the whole record as a single target — which is what a saturating-mutagenesis pool over one locus wants.
  • exclude_graf · boolean · optionnel
    drop guides matching a Graf 2019 inactive motif (the TT/GCC classes).
  • custom_prefix · string · optionnel
    your vector's 5' cloning overhang. BOTH sides must be given, or the pool stays on pLentiGuide — that is upstream's rule, reproduced. Advanced.
  • custom_suffix · string · optionnel
    your vector's 3' cloning overhang. Advanced.
  • exclude_poly_t · boolean · optionnel
    drop guides whose spacer carries a Pol-III (TTTT) terminator.
  • representation · number · optionnel
    cells you intend to keep carrying EACH guide. Joung et al. 2017 recommends >500; the default here is the neutral 1, not that recommendation, so the plan is the identity until you choose a scale. Advanced.
  • reads_per_oligo · number · optionnel
    sequencing reads per guide in the readout. Joung et al. 2017 recommends >500 for a screen (>100 to QC the cloned library); the default here is the neutral 1. Advanced.
  • guides_per_target · number · optionnel
    how many guides to take per target, best-ranked first.
  • restriction_enzymes · array · optionnel
    cloning enzymes whose recognition site must NOT appear in the spacer — a hit drops the guide from the pool. Advanced.
  • transduction_efficiency · number · optionnel
    fraction of cells that take up a construct, 0-1 — sizes the transduction back up from the cells you need to keep. Advanced.

  Exemple d'appel

  {"name": "crispr_design_library", "arguments": {"moi": 1, "rank": "ruleSet1", "_files": [], "_subject": {}, "nuclease": "SpCas9", "barcode_id": 1}}

  Exemple de retour

  {"content": [{"type": "text", "text": "…"}], "structuredContent": {"count": 1, "oligos": "texte", "coverage": "texte", "perTarget": "texte", "oligoLength": 1, "distinctSpacers": 1}}

• crispr_quantify_edits≈ 1280 tokens

  Quantify a CRISPR edit from a pair of Sanger traces — how much of the population was edited, what the indel spectrum looks like, and how well the model fits. Synthego ICE: the CONTROL trace gives the unedited sequence, the EDITED trace is decomposed into a mixture of proposed indels around each guide's cut, and the abundances are fitted. Answers the question a screen cannot: not whether a guide is good, but what it actually did to these cells.

  Paramètres, retour & exemple (8)

  Paramètres

  • donor · string · optionnel
    optional HDR donor / ssODN. Given one, ICE also proposes the recombination outcome and reports an HDR percentage; left empty there is no HDR arm rather than a zero.
  • _files · array · optionnel
    The project: record references shaped like _subject. Their records become library documents a tool names in sequences/parts/document; a trace or alignment is found by file name.
  • edited · string · requis
    the EDITED trace, by file name or id.
  • guides · array · requis
    the guide spacers, RNA accepted. Each is located in the CONTROL on either strand, so the cut sites come from the data rather than from a coordinate you supply.
  • control · string · requis
    the UNEDITED trace, by file name or id — it supplies the reference the edited read is decomposed against.
  • _subject · object · optionnel
    The record to act on: exactly one of sequence, accession (+source), sample (an id from list_samples) or file ({name, text} or {name, base64}); record_index picks one record of several.
  • base_editing · boolean · optionnel
    also fit every single-base change on the PAM-distal side of each cut, for a base editor. Left false, the scores stay comparable with published ICE numbers, which the extra proposals would move. Advanced.
  • indel_max_size · number · optionnel
    largest single-cut indel modeled either side of the cut — ICE's own CLI default is 20. In bp. Advanced.

  Exemple d'appel

  {"name": "crispr_quantify_edits", "arguments": {"edited": "texte", "guides": [], "control": "texte"}}

  Exemple de retour

  {"content": [{"type": "text", "text": "…"}], "structuredContent": {"iceD": 1, "checks": "texte", "hdrPct": 1, "report": "texte", "iceScore": 1, "perGuide": "texte", "rSquared": 1, "spectrum": "texte", "baseEdits": "texte", "inseparable": "texte", "contributions": "texte", "knockoutScore": 1}}

• crispr_score_deephf≈ 865 tokens

  Score CRISPR guides with DeepHF: a predicted knockout EFFICIENCY between 0 and 1 for wild-type SpCas9 (U6 or T7 promoter), eSpCas9(1.1) or SpCas9-HF1. It is not a z-score and not comparable with Rule Set 3 — the two answer different questions and must never be averaged or ranked together. Takes 23-nt protospacers (20-nt spacer + NGG PAM), which is what `crispr_design_guides` produces; a guide whose PAM is not canonical NGG comes back null rather than extrapolated, because the model was trained on NGG only. THE WEIGHTS DOWNLOAD ON FIRST USE, 3-5 MB per model, and scoring is slow by construction: each guide is folded twice, once with the 79-nt tracrRNA scaffold, before the network sees it.

  Paramètres, retour & exemple (4)

  Paramètres

  • model · string · optionnel · wt_u6 | wt_t7 | wt | esp | hf
    which published model to score under. This is a scientific choice about YOUR experiment — which Cas9 variant, and which promoter the sgRNA is expressed from — not a quality setting, and scores from two models are not comparable. Values: wt_u6 (WT SpCas9 · U6 promoter), wt_t7 (WT SpCas9 · T7 promoter), wt (WT SpCas9 · both promoters), esp (eSpCas9(1.1)), hf (SpCas9-HF1).
  • _files · array · optionnel
    The project: record references shaped like _subject. Their records become library documents a tool names in sequences/parts/document; a trace or alignment is found by file name.
  • _subject · object · optionnel
    The record to act on: exactly one of sequence, accession (+source), sample (an id from list_samples) or file ({name, text} or {name, base64}); record_index picks one record of several.
  • protospacers · array · requis
    the 23-nt protospacers to score — 20-nt spacer plus the 3-nt PAM, exactly as DeepHF takes them. Anything that is not 23 nt of unambiguous A/C/G/T ending in GG scores null rather than being silently trimmed or extrapolated.

  Exemple d'appel

  {"name": "crispr_score_deephf", "arguments": {"protospacers": []}}

  Exemple de retour

  {"content": [{"type": "text", "text": "…"}], "structuredContent": {"best": "texte", "model": "texte", "scored": 1, "scores": "texte", "efficiencies": "texte"}}

• crispr_score_deepspcas9≈ 753 tokens

  Score CRISPR guides with DeepSpCas9 (Kim et al. 2019, Sci Adv 5:eaax9249): a predicted INDEL FREQUENCY IN PERCENT for wild-type SpCas9. It is a third quantity, not a second opinion: Rule Set 3 is a z-score across a screen and DeepHF is an efficiency in [0, 1], so none of the three may be averaged or ranked together. Takes the 30-nt CONTEXT the model reads whole (4 nt + 20-nt spacer + 3-nt PAM + 3 nt), which is what `crispr_design_guides` reports as `context30`; a 23-nt protospacer is not enough and comes back null rather than padded. Unlike DeepHF it does NOT require a canonical NGG PAM, because its training library was not NGG-only. The output is the network's own linear value and is left unclipped, so a context it scores below zero reads below zero. THE WEIGHTS DOWNLOAD ON FIRST USE, about 0.93 MB, once.

  Paramètres, retour & exemple (3)

  Paramètres

  • _files · array · optionnel
    The project: record references shaped like _subject. Their records become library documents a tool names in sequences/parts/document; a trace or alignment is found by file name.
  • _subject · object · optionnel
    The record to act on: exactly one of sequence, accession (+source), sample (an id from list_samples) or file ({name, text} or {name, base64}); record_index picks one record of several.
  • contexts · array · requis
    the 30-nt contexts to score, exactly as DeepSpCas9 takes them: 4 nt upstream, the 20-nt spacer, the 3-nt PAM and 3 nt downstream. Anything that is not 30 nt of unambiguous A/C/G/T scores null, with the reason beside it, rather than being trimmed or padded.

  Exemple d'appel

  {"name": "crispr_score_deepspcas9", "arguments": {"contexts": []}}

  Exemple de retour

  {"content": [{"type": "text", "text": "…"}], "structuredContent": {"best": "texte", "scored": 1, "scores": "texte", "indelPercents": "texte"}}

• decompose_r_groups≈ 510 tokens

  RDKit's R-group decomposition of a list of small molecules on a core given as SMARTS (default RGroupDecomposition parameters): per matched structure its core and substituents R1, R2 …, and the structures the core does not match. Indices are 0-based.

  Paramètres, retour & exemple (4)

  Paramètres

  • core · string · requis
    the core, as SMARTS.
  • _files · array · optionnel
    The project: record references shaped like _subject. Their records become library documents a tool names in sequences/parts/document; a trace or alignment is found by file name.
  • _subject · object · optionnel
    The record to act on: exactly one of sequence, accession (+source), sample (an id from list_samples) or file ({name, text} or {name, base64}); record_index picks one record of several.
  • molecules · array · requis
    the structures: one SMILES or molfile per entry.

  Exemple d'appel

  {"name": "decompose_r_groups", "arguments": {"core": "texte", "molecules": []}}

  Exemple de retour

  {"content": [{"type": "text", "text": "…"}], "structuredContent": {"rows": "texte", "summary": "texte", "unmatched": "texte"}}

• delta_blast_smart≈ 894 tokens

  DELTA-BLAST, run on this machine: build a position-specific profile for a protein from the SMART conserved domains it contains, then search other proteins with it (one PSI-BLAST iteration) — more sensitive than BLASTP for distant homologs. Searches the open record's coding sequences unless `subjects` gives FASTA. NCBI BLAST+ 2.17.0's algorithms, checked against the deltablast program on every bundled protein. Nothing is sent anywhere.

  Paramètres, retour & exemple (9)

  Paramètres

  • _files · array · optionnel
    The project: record references shaped like _subject. Their records become library documents a tool names in sequences/parts/document; a trace or alignment is found by file name.
  • evalue · number · optionnel
    report alignments with E at most this (`-evalue`); BLAST's default is 10.
  • source · string · optionnel · bundled | ncbi
    where the SMART database is read from: 'bundled' (a byte-identical copy of NCBI's file) or 'ncbi' (NCBI's FTP site, now). Advanced.
  • protein · string · requis
    the protein, one-letter codes; wire it from translate_sequence or read it off a CDS.
  • _subject · object · optionnel
    The record to act on: exactly one of sequence, accession (+source), sample (an id from list_samples) or file ({name, text} or {name, base64}); record_index picks one record of several.
  • subjects · string · optionnel
    the proteins to search, as FASTA; leave empty to search the open record's coding sequences.
  • threshold · number · optionnel
    lowest profile word score seeded in the lookup table (`-threshold`). Advanced.
  • max_target_seqs · number · optionnel
    most proteins reported (`-max_target_seqs`).
  • domain_inclusion_evalue · number · optionnel
    conserved-domain hits with E below this build the profile (`-domain_inclusion_ethresh`).

  Exemple d'appel

  {"name": "delta_blast_smart", "arguments": {"protein": "texte"}}

  Exemple de retour

  {"content": [{"type": "text", "text": "…"}], "structuredContent": {"count": 1, "domains": "texte", "profile": "texte", "proteins": "texte"}}

• demultiplex_reads≈ 609 tokens

  Assign reads to the index each one came from, and say how many could NOT be assigned reliably — a hit further from a barcode than the set's guaranteed correction radius is not that barcode, and counting it as one is how a demultiplexing report hides a failed run.

  Paramètres, retour & exemple (5)

  Paramètres

  • reads · array · requis
    the observed index reads to assign.
  • _files · array · optionnel
    The project: record references shaped like _subject. Their records become library documents a tool names in sequences/parts/document; a trace or alignment is found by file name.
  • metric · string · optionnel · hamming | seqlev | levenshtein
    must match the error model the set was designed under. Values: hamming (Hamming (substitutions)), seqlev (Sequence-Levenshtein (indels)), levenshtein (Levenshtein).
  • _subject · object · optionnel
    The record to act on: exactly one of sequence, accession (+source), sample (an id from list_samples) or file ({name, text} or {name, base64}); record_index picks one record of several.
  • barcodes · array · requis
    the index set the reads were tagged with.

  Exemple d'appel

  {"name": "demultiplex_reads", "arguments": {"reads": [], "barcodes": []}}

  Exemple de retour

  {"content": [{"type": "text", "text": "…"}], "structuredContent": {"hits": "texte", "assigned": 1, "ambiguous": 1}}

• describe_discovery_corpus≈ 476 tokens

  The design step's view of a discovery corpus: each record's name, file, length and GC fraction, and how many records each file holds. Runs no test and returns no statistic, so hypotheses proposed from it are proposed before any result is seen (POPPER's metadata-only design step). Use it before run_discovery_programme.

  Paramètres, retour & exemple (3)

  Paramètres

  • _files · array · optionnel
    The project: record references shaped like _subject. Their records become library documents a tool names in sequences/parts/document; a trace or alignment is found by file name.
  • _subject · object · optionnel
    The record to act on: exactly one of sequence, accession (+source), sample (an id from list_samples) or file ({name, text} or {name, base64}); record_index picks one record of several.
  • sequences · array · optionnel
    the corpus: library document or file names, or wired records.

  Exemple d'appel

  {"name": "describe_discovery_corpus", "arguments": {"_files": [], "_subject": {}, "sequences": []}}

  Exemple de retour

  {"content": [{"type": "text", "text": "…"}], "structuredContent": {"files": "texte", "records": "texte"}}

• design_barcodes≈ 769 tokens

  Design a set of NGS sample-index barcodes with a guaranteed minimum distance, and report what that set actually corrects — substitutions, or indels too (DNABarcodes).

  Paramètres, retour & exemple (8)

  Paramètres

  • _files · array · optionnel
    The project: record references shaped like _subject. Their records become library documents a tool names in sequences/parts/document; a trace or alignment is found by file name.
  • length · number · optionnel
    barcode length in bases. In bp.
  • metric · string · optionnel · hamming | seqlev | levenshtein | phaseshift
    error model. A set correcting one substitution may correct zero indels, so this choice is the design, not a display option. Values: hamming (Hamming (substitutions)), seqlev (Sequence-Levenshtein (indels)), levenshtein (Levenshtein), phaseshift (Phaseshift).
  • _subject · object · optionnel
    The record to act on: exactly one of sequence, accession (+source), sample (an id from list_samples) or file ({name, text} or {name, base64}); record_index picks one record of several.
  • filter_gc · boolean · optionnel
    keep only balanced-GC barcodes (suppressed for length ≤ 3). Advanced.
  • heuristic · string · optionnel · conway | clique | sampling | ashlock
    set-construction strategy. Values: conway (Conway (greedy)), clique (Clique), sampling (Sampling), ashlock (Ashlock).
  • min_distance · number · optionnel
    required minimum distance between any two barcodes — this is what buys the error correction.
  • filter_triplets · boolean · optionnel
    reject barcodes containing a homotriplet (AAA…). Advanced.

  Exemple d'appel

  {"name": "design_barcodes", "arguments": {"_files": [], "length": 1, "metric": "hamming", "_subject": {}, "filter_gc": true, "heuristic": "conway"}}

  Exemple de retour

  {"content": [{"type": "text", "text": "…"}], "structuredContent": {"count": 1, "analysis": "texte", "barcodes": "texte", "warnings": "texte", "guarantee": "texte"}}

• design_bisulfite_primers≈ 1936 tokens

  Design BSP or MSP primers for a methylation assay, on the CONVERTED strands: after bisulfite treatment every unmethylated C reads as T, which is a different template from the one every other designer sees. BSP primers avoid CpGs so they amplify regardless of methylation state; MSP primers sit ON CpGs so they discriminate. Also reports the CpG islands (EMBOSS cpgplot) the assay should target.

  Paramètres, retour & exemple (25)

  Paramètres

  • assay · string · optionnel · BSP | MSP
    BSP = bisulfite sequencing PCR: primers avoid CpG sites so both methylated and unmethylated template amplify equally, and the methylation is read from the SEQUENCE afterwards. MSP = methylation-specific PCR: primers cover CpG sites so amplification ITSELF is the readout. They answer different questions and are not interchangeable. Values: BSP (BSP - amplify regardless of methylation), MSP (MSP - amplify only one state).
  • _files · array · optionnel
    The project: record references shaped like _subject. Their records become library documents a tool names in sequences/parts/document; a trace or alignment is found by file name.
  • max_gc · number · optionnel
    highest acceptable GC. In %. Advanced.
  • max_tm · number · optionnel
    primers above this Tm are rejected outright. In °C. Advanced.
  • min_gc · number · optionnel
    lowest acceptable GC. The floor is low on purpose: after conversion every unmethylated C is a T, so converted DNA is genuinely GC-poor and an ordinary 40% floor rejects correct primers. In %. Advanced.
  • min_tm · number · optionnel
    primers below this Tm are rejected outright. In °C. Advanced.
  • opt_tm · number · optionnel
    target Tm; candidates rank by distance from it. Bisulfite-converted DNA is C-poor, so these run lower than an ordinary design. In °C.
  • min_cpg · number · optionnel
    MSP ONLY. The fewest CpG sites a primer must cover, so it can discriminate methylated from unmethylated at all. In sites.
  • _subject · object · optionnel
    The record to act on: exactly one of sequence, accession (+source), sample (an id from list_samples) or file ({name, text} or {name, base64}); record_index picks one record of several.
  • criteria · string · optionnel · cpgplot | takaiJones
    which published criteria call a CpG island: Gardiner-Garden & Frommer 1987 as EMBOSS cpgplot encodes it, or the stricter Takai & Jones 2002, which excludes most Alu repeats. Values: cpgplot (Gardiner-Garden & Frommer (cpgplot)), takaiJones (Takai & Jones 2002 (promoter islands)).
  • max_length · number · optionnel
    longest primer considered. In nt. Advanced.
  • min_length · number · optionnel
    shortest primer considered. In nt. Advanced.
  • opt_length · number · optionnel
    primer length the ranking prefers. In nt.
  • region_end · number · optionnel
    0-based inclusive end. Unset = the whole sequence. Advanced.
  • max_results · number · optionnel
    how many primer pairs to return, best first.
  • product_max · number · optionnel
    longest acceptable amplicon. In bp.
  • product_min · number · optionnel
    shortest acceptable amplicon. In bp.
  • region_start · number · optionnel
    0-based inclusive start of the region to design in. Unset = the whole sequence; pass the selection's start to scope to it. Advanced.
  • island_window · number · optionnel
    sliding window over which C, G and CpG are counted (cpgplot -window); unset takes the preset's. In bp. Advanced.
  • min_non_cpg_c · number · optionnel
    BSP ONLY. The fewest non-CpG cytosines the ORIGINAL sequence under a primer must carry - the rule that makes a BSP primer bisulfite-SPECIFIC, because those cytosines become T only if conversion worked. A primer with none anneals to untreated DNA just as well and the assay silently reports on template that was never converted. In nt.
  • design_in_island · number · optionnel
    design inside this island only, by its rank in the reported list (1 = first). Unset designs anywhere in the region; the panel instead asks for an island to be picked.
  • island_min_length · number · optionnel
    minimum island length (cpgplot -minlen); unset takes the preset's. In bp. Advanced.
  • island_min_obs_exp · number · optionnel
    minimum observed/expected CpG (cpgplot -minoe); unset takes the preset's. Advanced.
  • island_min_percent · number · optionnel
    minimum %C+%G (cpgplot -minpc); unset takes the preset's. In %. Advanced.
  • max_cpg_distance_from_3 · number · optionnel
    MSP ONLY. How close to the 3' end the last CpG must sit. A mismatch discriminates most strongly at the 3' end, because that is where the polymerase extends. In nt. Advanced.

  Exemple d'appel

  {"name": "design_bisulfite_primers", "arguments": {"assay": "BSP", "_files": [], "max_gc": 1, "max_tm": 1, "min_gc": 1, "min_tm": 1}}

  Exemple de retour

  {"content": [{"type": "text", "text": "…"}], "structuredContent": {"assay": "texte", "count": 1, "pairs": "texte", "forward": "texte", "islands": "texte", "reverse": "texte", "islandCount": 1, "methylatedPairs": "texte", "unmethylatedPairs": "texte"}}

• design_codehop≈ 2183 tokens

  Design CODEHOP hybrid oligos from a block of aligned PROTEIN - for homologues too diverged for nucleotide-level design to see at all. Each primer is a 3' DEGENERATE core over a few conserved residues fused to a 5' non-degenerate consensus clamp, back-translated through a codon-usage table. A different algorithm from the degenerate designer, not a variant of it.

  Paramètres, retour & exemple (16)

  Paramètres

  • table · string · requis
    the codon-usage table to back-translate the clamp through, BY NAME as the Codon Usage panel lists it. REQUIRED and deliberately without a default: a CODEHOP designed under the wrong organism's usage is wrong in a way nothing downstream can detect, so picking one here would silently pick a host (§1).
  • _files · array · optionnel
    The project: record references shaped like _subject. Their records become library documents a tool names in sequences/parts/document; a trace or alignment is found by file name.
  • strand · string · optionnel · forward | reverse | both
    which strand to design on. `both` returns forward and reverse sets, which is what a PCR needs.
  • max_run · number · optionnel
    longest single-base run allowed; 2003's stated polynucleotide run limit. A primer exceeding it is rejected. In nt. Advanced.
  • _subject · object · optionnel
    The record to act on: exactly one of sequence, accession (+source), sample (an id from list_samples) or file ({name, text} or {name, base64}); record_index picks one record of several.
  • clamp_tm · number · optionnel
    target melting temperature for the non-degenerate 5' clamp (Rose 2003 step 8: "the current default is 60 °C, which usually provides a clamp of ~20 nucleotides"), measured as nearest-neighbour Tm in the buffer `conditions` names. In °C.
  • alignment · array · optionnel
    the ALIGNED PROTEIN rows, each { name, sequence } in one-letter amino acids with gaps preserved - wire an upstream protein alignment here. At least 3 sequences: the clamp is a CONSENSUS, and two have none worth the name.
  • weighting · string · optionnel · pb | none
    how the alignment's rows are weighted before the core's consensus is read. Values: pb (Position-based (Henikoff & Henikoff 1994)), none (None — every row counts once). Advanced.
  • conditions · object · optionnel
    salt, magnesium, dNTP and oligo concentrations plus the salt-correction method and any additives the clamp Tm is measured in. Left unset it is filled from your reaction-conditions settings, and falls back to pydna's Taq defaults (SantaLucia & Hicks 2004 table, 250 nM primer, Owczarzy 2008 salt correction) when there are none. Advanced.
  • base_cutoff · number · optionnel
    minimum predicted probability for a base to enter the degenerate core. Advanced.
  • block_index · number · optionnel
    which gapless block to design in, 0-based, ordered as `gaplessBlocks` returns them (blocks of at least 8 ungapped columns). Unset = the first.
  • core_lengths · array · optionnel
    core lengths the scan tries, in residues — every length here is scanned and the best-scoring core kept. Advanced.
  • alignment_fasta · string · optionnel
    an aligned PROTEIN FASTA, when there is no upstream alignment to wire.
  • genetic_code_id · number · optionnel
    NCBI `transl_table` id for the codon-to-residue map. Advanced.
  • max_clamp_length · number · optionnel
    ceiling on clamp growth, so an unreachable Tm REFUSES instead of consuming the whole block. Ours, and a stop condition rather than a published criterion - 40 nt is already twice the ~20 the paper expects. In nt. Advanced.
  • max_core_degeneracy · number · optionnel
    degeneracy ceiling for the 3' core (Rose 2003 step 7: "a maximum degeneracy of 128").

  Exemple d'appel

  {"name": "design_codehop", "arguments": {"table": "texte"}}

  Exemple de retour

  {"content": [{"type": "text", "text": "…"}], "structuredContent": {"table": "texte", "forward": "texte", "primers": "texte", "reverse": "texte", "blockCount": 1, "rejections": "texte", "primerCount": 1}}

• design_degenerate_primers≈ 1592 tokens

  Design degenerate primers from a multiple-sequence ALIGNMENT - the 'amplify every homologue in this family' question, which a single-template designer cannot answer because it only ever sees one sequence. A faithful port of DegePrime (Hugerth et al. 2014). Wire an upstream align_sequences `rows` output straight in, or paste an aligned FASTA.

  Paramètres, retour & exemple (17)

  Paramètres

  • seed · number · optionnel
    seed for WRM's draw, so a run is REPRODUCIBLE. Upstream is unseeded, so the same alignment can give two answers; a design you cannot reproduce is not one you can order from. Only applies when algorithm is wrm. Advanced.
  • skip · number · optionnel
    bases excluded at each end of every sequence (`-skip`). In nt. Advanced.
  • limit · number · optionnel
    how many pairs to return, best coverage first. Advanced.
  • _files · array · optionnel
    The project: record references shaped like _subject. Their records become library documents a tool names in sequences/parts/document; a trace or alignment is found by file name.
  • length · number · optionnel
    oligomer length (DegePrime `-l`). In nt.
  • _subject · object · optionnel
    The record to act on: exactly one of sequence, accession (+source), sample (an id from list_samples) or file ({name, text} or {name, base64}); record_index picks one record of several.
  • algorithm · string · optionnel · wrm | summation | expansion | constriction | exhaustive
    which search picks each window's oligo. `wrm` is DegePrime's own default and is randomised (hence `seed`); `exhaustive` is an exact branch-and-bound that GRADES the heuristics rather than letting them grade each other, and REFUSES a window too large to solve rather than guessing - the problem is NP-hard.
  • alignment · array · optionnel
    the ALIGNED rows to scan, each `{ name, sequence }` with gaps preserved - wire an upstream `align_sequences` rows output here. Gaps carry information the scan reads, so an unaligned set is not a substitute.
  • min_depth · number · optionnel
    fewest gapless sequences a window needs before it is reported at all (`-depth`). Advanced.
  • iterations · number · optionnel
    WRM restarts (`-iter`). Only applies when algorithm is wrm. Advanced.
  • max_product · number · optionnel
    longest product, in TRIMMED alignment columns. In col.
  • min_product · number · optionnel
    shortest product, in TRIMMED alignment columns. In col.
  • trim_cutoff · number · optionnel
    columns occupied by less than this fraction of sequences are dropped before scanning. Trimming renumbers the alignment, which is why `keptColumns` comes back with the result. Advanced.
  • max_degeneracy · number · optionnel
    degeneracy ceiling (`-d`) - how many distinct oligos the IUPAC code is allowed to stand for. Coerced DOWN when no combination of positions can multiply to it, and the run says so.
  • alignment_fasta · string · optionnel
    an aligned FASTA to scan, when there is no upstream alignment to wire. Sequences must already BE aligned - equal length, gaps as `-`.
  • exhaustive_mer_limit · number · optionnel
    largest number of distinct mers `exhaustive` will attempt before refusing a window. Only applies when algorithm is exhaustive. Advanced.
  • min_fraction_matching · number · optionnel
    a window must bind at least this fraction of the spanning sequences to be a candidate - the coverage floor, and the number that decides whether 'every homologue' is true.

  Exemple d'appel

  {"name": "design_degenerate_primers", "arguments": {"seed": 1, "skip": 1, "limit": 1, "_files": [], "length": 1, "_subject": {}}}

  Exemple de retour

  {"content": [{"type": "text", "text": "…"}], "structuredContent": {"pairs": "texte", "forward": "texte", "reverse": "texte", "windows": "texte", "pairCount": 1, "keptColumns": "texte", "degeneracyCoerced": true, "maxDegeneracyUsed": 1}}

• design_expression_variants≈ 1910 tokens

  The expression-design deliverable: several coding sequences for one protein, each variant following a different published strategy (maximise codon adaptation, match the host's codon usage, harmonise with the native host, or preserve the initiation region), each scored by an engine — CAI, GC, the folding energy of the Kudla -4..+37 initiation window, and rare codons. It returns the comparison rather than one answer, because the strategies disagree about what limits expression and the researcher picks. Refuses a frame-shifted CDS, an internal stop or a missing host table rather than optimising nonsense.

  Paramètres, retour & exemple (18)

  Paramètres

  • cds · string · optionnel
    the coding sequence to redesign, in frame and start-codon first. Unset falls back to THE SELECTION, on the strand the selection or its matching annotation states, then to the whole open record.
  • seed · number · optionnel
    seed for the solver's random draws, so a listed variant can be regenerated exactly. Advanced.
  • _files · array · optionnel
    The project: record references shaped like _subject. Their records become library documents a tool names in sequences/parts/document; a trace or alignment is found by file name.
  • gc_max · number · optionnel
    maximum GC fraction (0-1); set with gc_min. Advanced.
  • gc_min · number · optionnel
    minimum GC fraction (0-1); set with gc_max. Advanced.
  • feature · string · optionnel
    redesign this annotated CDS or gene by NAME instead of the selection, exactly as `codon_usage_analysis` takes one. Its own strand is used. Takes precedence over the selection; `cds` still wins over both.
  • _subject · object · optionnel
    The record to act on: exactly one of sequence, accession (+source), sample (an id from list_samples) or file ({name, text} or {name, base64}); record_index picks one record of several.
  • postures · array · requis
    which strategies to design, in order. max_cai = every amino acid takes the target host's single most-used codon; match_usage = reproduce the target host's synonymous-codon distribution rather than its single best codon, so rare codons stay at their natural rate; harmonize = put each codon at the same relative adaptiveness it had in the gene's native host, so the elongation rhythm (and any pause the protein folds around) survives the transfer; native_initiation = leave nt +1…+37 of the coding sequence exactly as they are and match the host's codon usage only downstream, so the redesign cannot add secondary structure to the window Kudla found dominant. The set IS the deliverable — asking for one gets one, and there is no hidden default of three.
  • upstream · string · optionnel
    the bases immediately 5' of the CDS (the 5'UTR/RBS region). Kudla's window starts 4 nt BEFORE the start codon, so without this the folding energy is reported over a truncated window and says so.
  • gc_window · number · optionnel
    window in bp the GC bounds apply over (whole sequence when unset). Advanced.
  • host_table · string · optionnel
    the TARGET host's codon-usage table, BY NAME, as the Codon Usage panel lists it. This is the way to pass a table: it resolves against the tables loaded in this project, so the numbers come from a table someone built or fetched. Leave unset and the active table is used.
  • rare_below · number · optionnel
    within-family frequency below which a codon counts as RARE, for the report only — it adds no constraint. Omit and no rare-codon count is reported, which is the honest answer: "rare" has no host-independent definition.
  • native_table · string · optionnel
    the gene's NATIVE host codon table, BY NAME from this project's loaded tables — required only for the `harmonize` posture, which matches relative adaptiveness BETWEEN two hosts. It must be a DIFFERENT table from `host_table`: harmonising a host against itself is a difference of zero.
  • genetic_table · string · optionnel
    genetic code for the translation constraint (default Standard). Advanced.
  • avoid_patterns · array · optionnel
    literal patterns (restriction sites, homopolymers) every variant must not contain.
  • host_table_tsv · string · optionnel
    ONLY for a table you are pasting yourself, measured elsewhere — prefer `host_table`, which names one this project already has. Do NOT write a table out from memory: codon frequencies are measured data, and a typed one is indistinguishable from a real one in the result. TSV: codon<TAB>count. Advanced.
  • host_table_name · string · optionnel
    how to name that table on every score it produced (e.g. "E. coli K-12, Kazusa"), so a reported CAI is attributable.
  • native_table_tsv · string · optionnel
    ONLY for a native table you are pasting yourself — prefer `native_table`. Do not write one out from memory (see `host_table_tsv`). TSV: codon<TAB>count. Advanced.

  Exemple d'appel

  {"name": "design_expression_variants", "arguments": {"postures": []}}

  Exemple de retour

  {"content": [{"type": "text", "text": "…"}], "structuredContent": {"region": "texte", "report": "texte", "protein": "texte", "records": "texte", "skipped": "texte", "best_cai": "texte", "distinct": 1, "variants": "texte", "least_structured": "texte"}}

• design_free_codes≈ 959 tokens

  Generate INDEL-correcting barcodes — FREE divergence codes (Hawkins et al., PNAS 2018) — by reserving each codeword's error sphere over the whole 4^k space, so the guarantee survives an insertion or deletion rather than only a substitution. Or prune a set you already own down to a valid FREE code, and see which members' decode spheres collided. This is a different construction from design_barcodes' distance-based search, and answers a different question: a Levenshtein-distance set corrects indels between two barcodes, a FREE code corrects them in the read.

  Paramètres, retour & exemple (10)

  Paramètres

  • mode · string · optionnel · generate | prune
    generate a new code, or prune an existing set down to a valid one. Values: generate (Generate a code), prune (Prune a set to a valid code).
  • limit · number · optionnel
    stop after this many codewords. 0 = take the whole code. Advanced.
  • _files · array · optionnel
    The project: record references shaped like _subject. Their records become library documents a tool names in sequences/parts/document; a trace or alignment is found by file name.
  • length · number · optionnel
    barcode length k. The search is over the whole 4^k space, so cost rises steeply with it.
  • max_gc · number · optionnel
    reject a candidate above this GC fraction. 0 = no limit. Advanced.
  • _subject · object · optionnel
    The record to act on: exactly one of sequence, accession (+source), sample (an id from list_samples) or file ({name, text} or {name, base64}); record_index picks one record of several.
  • barcodes · array · optionnel
    the set to prune — required when `mode` is `prune`, ignored when generating. Only applies when mode is prune.
  • reserved · array · optionnel
    codewords already in use, whose decode spheres are claimed BEFORE generation — this is how a code is EXTENDED rather than regenerated, so what comes back is compatible with the indexes a lab already owns.
  • max_errors · number · optionnel
    how many insertions/deletions/substitutions each codeword must tolerate. Each extra error costs most of the code.
  • max_homopolymer · number · optionnel
    reject a candidate with a run of this many identical bases. 0 = no limit. Advanced.

  Exemple d'appel

  {"name": "design_free_codes", "arguments": {"mode": "generate", "limit": 1, "_files": [], "length": 1, "max_gc": 1, "_subject": {}}}

  Exemple de retour

  {"content": [{"type": "text", "text": "…"}], "structuredContent": {"count": 1, "dropped": "texte", "barcodes": "texte"}}

• design_fusion_site_primers≈ 875 tokens

  Design the PCR primers that ADD Type-IIS fusion sites to a part: enzyme site, spacer and the four-base overhang you chose, on a Tm-matched annealing footprint. This is how a sequence that is not yet a Golden Gate part becomes one, and it is the other half of check_golden_gate_parts — that says which parts are unusable, this makes one usable.

  Paramètres, retour & exemple (8)

  Paramètres

  • _files · array · optionnel
    The project: record references shaped like _subject. Their records become library documents a tool names in sequences/parts/document; a trace or alignment is found by file name.
  • enzyme · string · optionnel
    the Type-IIS enzyme the assembly will use.
  • _subject · object · optionnel
    The record to act on: exactly one of sequence, accession (+source), sample (an id from list_samples) or file ({name, text} or {name, base64}); record_index picks one record of several.
  • sequence · string · optionnel
    the template to amplify — wire a record, name a library document, or leave unset to use the open record.
  • target_tm · number · optionnel
    target annealing temperature for the template-binding footprint. In °C.
  • buffer_bases · string · optionnel
    5' buffer bases outside the recognition site, so the enzyme has somewhere to sit (NEB recommends 6 nt). Advanced.
  • left_overhang · string · requis
    the top-strand overhang to leave at the START of the released part — its length must match the enzyme's own overhang.
  • right_overhang · string · requis
    the top-strand overhang to leave at the END of the released part.

  Exemple d'appel

  {"name": "design_fusion_site_primers", "arguments": {"left_overhang": "texte", "right_overhang": "texte"}}

  Exemple de retour

  {"content": [{"type": "text", "text": "…"}], "structuredContent": {"forward": "texte", "product": "texte", "reverse": "texte", "forwardTm": 1, "reverseTm": 1, "releasedPart": "texte"}}

• design_genetic_circuit≈ 1280 tokens

  Design a genetic circuit that computes: give it a logic function and it synthesizes a NOR/NOT netlist, assigns real characterized repressor gates from a Cello UCF library, predicts the dynamic range between ON and OFF, and emits the construct's DNA. The gate parameters are MEASURED, from the published libraries, with the host and growth conditions they were measured under reported alongside — never estimated here.

  Paramètres, retour & exemple (8)

  Paramètres

  • logic · string · optionnel
    the function the circuit computes: a named gate (NOT, AND, OR, NAND, NOR, XOR, XNOR, AND3, OR3, MAJORITY-3), or a truth table as one bit per input combination with the first input most significant (AND is `0001`).
  • _files · array · optionnel
    The project: record references shaped like _subject. Their records become library documents a tool names in sequences/parts/document; a trace or alignment is found by file name.
  • groups · string · optionnel
    comma-separated repressor groups the search may draw on. Narrowing this is how a large search is made tractable — and how a gate you cannot obtain is kept out of the design. Advanced.
  • library · string · optionnel · Bth1C1G1T1 | Eco1C1G1T1 | Eco1C2G2T2 | Eco2C1G3T1 | Eco2C1G5T1 | SC1C1G1T1
    the characterized gate library to build from. Each was measured in one host under one growth condition, and the prediction inherits both.
  • sensors · string · optionnel
    comma-separated input sensors the search may use. Leave unset to consider every sensor the library carries. Advanced.
  • _subject · object · optionnel
    The record to act on: exactly one of sequence, accession (+source), sample (an id from list_samples) or file ({name, text} or {name, base64}); record_index picks one record of several.
  • reporters · string · optionnel
    comma-separated output reporters the search may use. Leave unset to consider all of them. Advanced.
  • max_assignments · number · optionnel
    refuse rather than search past this many assignments. A ceiling, not a target: the search is EXHAUSTIVE, so it is never sampled — a best-of-some reported as a best-of-all is a wrong answer rather than a slow one. Advanced.

  Exemple d'appel

  {"name": "design_genetic_circuit", "arguments": {"logic": "texte", "_files": [], "groups": "texte", "library": "Bth1C1G1T1", "sensors": "texte", "_subject": {}}}

  Exemple de retour

  {"content": [{"type": "text", "text": "…"}], "structuredContent": {"dna": "texte", "score": 1, "curves": "texte", "netlist": "texte", "sequence": "texte", "toxicity": "texte", "libraries": "texte", "placement": "texte", "assignment": "texte", "truthTable": "texte", "explanation": "texte"}}

• design_gibson_primers≈ 1809 tokens

  Design the PCR primers that CREATE the terminal homology a Gibson/NEBuilder/In-Fusion assembly needs: a Tm-matched pair per fragment, each carrying the 5' overhang that fuses it to its neighbour in the order given (pydna assembly_fragments). This is the step that turns a planned assembly into oligos you can order.

  Paramètres, retour & exemple (10)

  Paramètres

  • _files · array · optionnel
    The project: record references shaped like _subject. Their records become library documents a tool names in sequences/parts/document; a trace or alignment is found by file name.
  • overlap · number · optionnel
    homology shared between two adjacent fragments. pydna splits it across the junction, so each primer's 5' tail is about half this. In bp.
  • _subject · object · optionnel
    The record to act on: exactly one of sequence, accession (+source), sample (an id from list_samples) or file ({name, text} or {name, base64}); record_index picks one record of several.
  • circular · boolean · optionnel
    close the ring: the last fragment also overlaps the first.
  • fragments · array · optionnel
    the fragments to join, IN ASSEMBLY ORDER — wire upstream `record` outputs here, or list library document names/ids.
  • target_tm · number · optionnel
    target annealing Tm for each primer's 3' footprint. In °C.
  • conditions · object · optionnel
    salt, magnesium, dNTP and oligo concentrations plus the salt-correction method the target Tm is measured in. Left unset it is filled from your reaction-conditions settings, and falls back to pydna's Taq defaults when there are none. Advanced.
  • min_footprint · number · optionnel
    shortest annealing footprint the designer may settle for (pydna's `limit`). In nt. Advanced.
  • include_subject · boolean · optionnel
    put the node's subject first, as the backbone.
  • synthesis_scale · string · optionnel
    catalogue product to price the oligos at (an `oligo-list-prices` record id); `auto` prices each at the cheapest product whose published length range covers it. Advanced.

  Exemple d'appel

  {"name": "design_gibson_primers", "arguments": {"_files": [], "overlap": 1, "_subject": {}, "circular": true, "fragments": [], "target_tm": 1}}

  Exemple de retour

  {"content": [{"type": "text", "text": "…"}], "structuredContent": {"cost": "texte", "overlap": 1, "primers": "texte", "circular": true, "amplicons": "texte", "costTotal": 1, "conditions": "texte", "primerCount": 1}}

• design_hcr_probes≈ 1295 tokens

  Design HCR v3.0 split-initiator probe pairs against the subject: tile its reverse complement into 52 nt windows, drop windows with C or G runs, a stable hairpin, G+C or RNA:DNA free energy outside their windows, or (given a bowtie2 alignment of the tiles) more than one genome hit, then pick non-overlapping tiles closest to the target free energy and split each around a 2 nt gap into an odd and an even probe carrying half of the chosen amplifier's initiator. Each stage reports how many tiles it kept.

  Paramètres, retour & exemple (17)

  Paramètres

  • _files · array · optionnel
    The project: record references shaped like _subject. Their records become library documents a tool names in sequences/parts/document; a trace or alignment is found by file name.
  • max_gc · number · optionnel
    highest percent G+C of a tile. In %.
  • min_gc · number · optionnel
    lowest percent G+C of a tile. In %.
  • channel · string · optionnel · B1 | B2 | B3 | B4 | B5
    HCR amplifier whose split initiator the pair carries; one channel per target in a multiplexed experiment.
  • dtm_max · number · optionnel
    largest allowed difference between the halves' melting temperatures. In °C. Only applies when dtm_filter is true. Advanced.
  • _subject · object · optionnel
    The record to act on: exactly one of sequence, accession (+source), sample (an id from list_samples) or file ({name, text} or {name, base64}); record_index picks one record of several.
  • max_gibbs · number · optionnel
    least stable RNA:DNA free energy to accept. In kcal/mol.
  • min_gibbs · number · optionnel
    most stable RNA:DNA free energy to accept (at 37 °C, 0.33 M Na⁺). In kcal/mol.
  • tile_size · number · optionnel
    length of the target window each pair covers, both halves and the 2 nt gap. In nt. Advanced.
  • dtm_filter · boolean · optionnel
    also require the two halves' melting temperatures to agree. Advanced.
  • max_probes · number · optionnel
    most probe pairs to return.
  • target_gibbs · number · optionnel
    free energy the selection ranks tiles by closeness to. In kcal/mol.
  • alignment_sam · string · optionnel
    SAM from bowtie2 -k 3 -f of the tiles FASTA this tool returns, against your genome or transcriptome. Without it no tile is checked for uniqueness and the result says so.
  • max_hairpin_tm · number · optionnel
    drop a tile whose primer3 hairpin melts at or above this. In °C. Advanced.
  • max_run_length · number · optionnel
    window length for the C and G run check. In nt. Advanced.
  • num_hits_allowed · number · optionnel
    most alignments a tile may have and still be kept (its own locus counts as one). Only applies when alignment_sam is set.
  • max_run_mismatches · number · optionnel
    bases in that window allowed to differ from the run base. In nt. Advanced.

  Exemple d'appel

  {"name": "design_hcr_probes", "arguments": {"_files": [], "max_gc": 1, "min_gc": 1, "channel": "B1", "dtm_max": 1, "_subject": {}}}

  Exemple de retour

  {"content": [{"type": "text", "text": "…"}], "structuredContent": {"pairs": "texte", "stages": "texte", "pairCount": 1, "orderTable": "texte", "tilesFasta": "texte", "explanation": "texte"}}

• design_ish_probes≈ 2235 tokens

  Design an in-situ hybridization probe against the subject: tile it into candidate oligos that meet a melting-temperature, G+C and composition specification, screen them for off-target binding against an alignment and for k-mers abundant in a reference, and gather the survivors into the set that images best. Merges OligoMiner's tiling, its trained specificity model and its k-mer filter with iFISH's probe-set selection; each stage reports what it removed and why.

  Paramètres, retour & exemple (30)

  Paramètres

  • dnac1 · number · optionnel
    concentration of the higher-concentration strand, typically the probe, in the melting-temperature calculation (OligoMiner `--dnac1`). In nM.
  • dnac2 · number · optionnel
    concentration of the lower-concentration strand, typically the target (OligoMiner `--dnac2`). The Tm uses dnac1 − dnac2/2, so equal values halve the effective concentration. In nM.
  • _files · array · optionnel
    The project: record references shaped like _subject. Their records become library documents a tool names in sequences/parts/document; a trace or alignment is found by file name.
  • max_gc · number · optionnel
    highest percent G+C to accept. In %.
  • max_tm · number · optionnel
    highest melting temperature to accept. In °C.
  • min_gc · number · optionnel
    lowest percent G+C to accept. In %.
  • min_tm · number · optionnel
    lowest melting temperature to accept, AFTER the formamide correction. In °C.
  • origin · number · optionnel
    coordinate of the subject's first base, when it is a window cut from a larger sequence. Read from a UCSC-style `range=` header when the subject carries one. Advanced.
  • probes · number · optionnel
    how many probe sets to return. Only applies when oligos_per_probe is set.
  • sodium · number · optionnel
    monovalent cation concentration of the hybridization buffer. In mM.
  • overlap · boolean · optionnel
    report every window that qualifies, including overlapping ones. Off by default because overlapping oligos cannot be used together in one probe. Advanced.
  • rank_by · string · optionnel · centrality | size | homogeneity
    feature that ranks the sets inside that band. Values: centrality (Centrality on the region), size (Compactness), homogeneity (Even spacing). Only applies when oligos_per_probe is set. Advanced.
  • spacing · number · optionnel
    bases forced between consecutive oligos. In nt. Advanced.
  • _subject · object · optionnel
    The record to act on: exactly one of sequence, accession (+source), sample (an id from list_samples) or file ({name, text} or {name, base64}); record_index picks one record of several.
  • filter_by · string · optionnel · centrality | size | homogeneity
    feature that defines the band of acceptable sets. Values: centrality (Centrality on the region), size (Compactness), homogeneity (Even spacing). Only applies when oligos_per_probe is set. Advanced.
  • formamide · number · optionnel
    formamide in the hybridization buffer; it lowers every melting temperature by about 0.65 °C per percent. In %.
  • kmer_dump · string · optionnel
    `jellyfish dump` of a genome's k-mer dictionary, for a reference too large to count here: `jellyfish count -m 18 -L 5` then `jellyfish dump -c -L 5` keeps only the k-mers a screen at 5 acts on. Advanced.
  • max_length · number · optionnel
    longest oligo to accept; the tiler grows a window until one fits, so a wide range yields more probes. In nt.
  • min_length · number · optionnel
    shortest oligo to accept. In nt.
  • prohibited · string · optionnel
    comma-separated subsequences an oligo may not contain; the default bans homopolymer runs, which hybridize promiscuously. Advanced.
  • kmer_length · number · optionnel
    k, the k-mer length counted in kmer_reference (OligoMiner's README builds 18); a dump carries its own. In nt. Only applies when kmer_reference is set.
  • screen_mode · string · optionnel · lda | unique | zero
    trained model (recovers usable probes near repeats) · unique alignment only (strict) · no alignment at all (for a sequence that should be absent). Values: lda (Trained model), unique (Unique alignment only), zero (No alignment at all). Only applies when alignment_sam is set.
  • alignment_sam · string · optionnel
    SAM the candidates were aligned with, for off-target screening. Without it the oligos are returned UNSCREENED and the result says so.
  • kmer_canonical · boolean · optionnel
    count a k-mer and its reverse complement as one (jellyfish -C). Off as OligoMiner's dictionary is; for a dump it must match how the dictionary was counted. Advanced.
  • kmer_reference · string · optionnel
    FASTA of the reference to count k-mers in, for OligoMiner's k-mer screen. Counted here, so a whole genome belongs in kmer_dump instead. Without either the oligos are returned with k-mer abundance UNCHECKED and the result says so.
  • kmer_threshold · number · optionnel
    drop an oligo holding any k-mer that occurs this many times or more in the reference.
  • filter_threshold · number · optionnel
    width of the band around the best set, as a fraction of its own value. Only applies when oligos_per_probe is set. Advanced.
  • oligos_per_probe · number · optionnel
    oligos to gather into one probe. Leave unset to return every surviving oligo instead of a set.
  • hybridization_temperature · number · optionnel · 32 | 37 | 42 | 47 | 52 | 57
    temperature the specificity model was trained at. Only these six exist; the coefficients change sign across the range, so an intermediate value is a different model rather than a blend. In °C. Only applies when alignment_sam is set.
  • max_off_target_probability · number · optionnel
    keep an oligo whose modelled chance of a real off-target site is below this. Only applies when alignment_sam is set. Advanced.

  Exemple d'appel

  {"name": "design_ish_probes", "arguments": {"dnac1": 1, "dnac2": 1, "_files": [], "max_gc": 1, "max_tm": 1, "min_gc": 1}}

  Exemple de retour

  {"content": [{"type": "text", "text": "…"}], "structuredContent": {"kmer": "texte", "oligos": "texte", "probes": "texte", "stages": "texte", "coverage": "texte", "oligoCount": 1, "explanation": "texte", "coveredFraction": 1}}

• design_knockout_package≈ 1719 tokens

  The complete build package for a knockout or knock-in, as one object: guides inside the target, an off-target census for the chosen one within this molecule, a repair template with real homology arms, a screening PCR whose primers sit OUTSIDE the arms, the protocol in order, the fragments and oligos to buy, and every coordinate ready for the map. Two donor modes: by default the arms sit on the cut (a point insertion — the target's own sequence is kept on both sides), and with `replace_target` the arms flank the whole target and it is deleted, which is the mode for replacing one CDS with another (an empty insert then deletes the target cleanly). It refuses rather than guessing: no PAM in the target, arms that run off a linear molecule, a screening amplicon that cannot clear the arms, or a non-DNA insert; and in the default mode it WARNS when an insert lands inside the target, because that is a fusion rather than a replacement. Arm length, screening flank and guide count are yours to state, because each follows the delivery method and the organism.

  Paramètres, retour & exemple (16)

  Paramètres

  • _files · array · optionnel
    The project: record references shaped like _subject. Their records become library documents a tool names in sequences/parts/document; a trace or alignment is found by file name.
  • guides · number · optionnel
    how many guides to carry into the package, best-scoring first. The rest are the alternatives, not filler.
  • insert · string · optionnel
    sequence to place at the cut (a tag, a selection cassette). Leave empty for a scarless rejoin — the package then WARNS that the two screening products are the same length.
  • subject · string · optionnel
    the molecule to edit — wire a record or name a library document; leave unset to edit the open record.
  • _subject · object · optionnel
    The record to act on: exactly one of sequence, accession (+source), sample (an id from list_samples) or file ({name, text} or {name, base64}); record_index picks one record of several.
  • nuclease · string · optionnel · SpCas9 | SpCas9-NG | SpG | SpRY | xCas9 | SaCas9 | SaCas9-KKH | AsCas12a
    the nuclease (PAM + spacer length) to scan the target for. Values: SpCas9 (SpCas9: NGG (3')), SpCas9-NG (SpCas9-NG: NG (3')), SpG (SpG: NGN (3')), SpRY (SpRY: NRN (3')), xCas9 (xCas9: NG (3')), SaCas9 (SaCas9: NNGRRT (3')), SaCas9-KKH (SaCas9-KKH: NNNRRT (3')), AsCas12a (AsCas12a: TTTV (5')), LbCas12a (LbCas12a: TTTV (5')), enAsCas12a (enAsCas12a: TTTV (5')).
  • primer_tm · number · optionnel
    target melting temperature for the screening primers [°C] — follows your polymerase and buffer. In °C. Advanced.
  • arm_length · number · requis
    homology-arm length on EACH side of the cut, in bp. A protocol decision that follows the delivery method, so there is no default: state what yours needs. The published working range is 100-800 (100-400 nt synthetic, up to ~800 bp cloned). In bp.
  • target_end · number · requis
    end of the gene to knock out (0-based, exclusive). In bp.
  • insert_name · string · optionnel
    what the insert is called in the protocol and on the order form.
  • target_name · string · optionnel
    what the target is called, so every mark, primer and order line names its subject.
  • screen_flank · number · requis
    how far OUTSIDE the arms the screening primers must bind, in bp. Not decoration: a primer inside the arms amplifies the repair template as readily as the locus, so the assay cannot tell an edited colony from plasmid carry-over. In bp.
  • target_start · number · requis
    start of the gene to knock out (0-based, inclusive). In bp.
  • max_mismatches · number · optionnel
    mismatch ceiling for the off-target search within this molecule. Advanced.
  • replace_target · boolean · optionnel
    replace the WHOLE target region with the insert, arms flanking the target — the gene-replacement donor. Off (default): the arms sit on the cut and the target's own sequence is kept on both sides of the insert (a point insertion), so this must be ON to knock one CDS in for another. Empty insert + this = a clean deletion of the target. Advanced.
  • restriction_enzymes · array · optionnel
    cloning enzymes whose recognition site must NOT appear in a spacer. Advanced.

  Exemple d'appel

  {"name": "design_knockout_package", "arguments": {"arm_length": 1, "target_end": 1, "screen_flank": 1, "target_start": 1}}

  Exemple de retour

  {"content": [{"type": "text", "text": "…"}], "structuredContent": {"donor": "texte", "marks": "texte", "order": "texte", "steps": [], "chosen": "texte", "guides": "texte", "record": {}, "report": "texte", "screening": "texte", "offTargets": "texte"}}

• design_lamp_primers≈ 1895 tokens

  Design LAMP (loop-mediated isothermal amplification) primer SETS - four core oligos (F3 · B3 · FIP · BIP) plus optional loop primers, judged against Eiken's own PrimerExplorer V5 criteria. Not a pair: LAMP needs six binding regions in the published order and the distances BETWEEN them are as much of the design as the oligos. Each set comes back with the arithmetic behind its rank.

  Paramètres, retour & exemple (24)

  Paramètres

  • _files · array · optionnel
    The project: record references shaped like _subject. Their records become library documents a tool names in sequences/parts/document; a trace or alignment is found by file name.
  • gc_max · number · optionnel
    GC FRACTION window, 0-1 (manual §2.3: "between about 40% to 65%") - upper bound. Unset = the preset for this template's GC class. Advanced.
  • gc_min · number · optionnel
    GC FRACTION window, 0-1 (manual §2.3: "between about 40% to 65%") - lower bound. Unset = the preset for this template's GC class. Advanced.
  • _subject · object · optionnel
    The record to act on: exactly one of sequence, accession (+source), sample (an id from list_samples) or file ({name, text} or {name, base64}); record_index picks one record of several.
  • max_sets · number · optionnel
    how many sets to return, best first.
  • length_max · number · optionnel
    length window for the outer/inner binding regions (manual §4.2) - upper bound. Unset = the preset for this template's GC class. In nt. Advanced.
  • length_min · number · optionnel
    length window for the outer/inner binding regions (manual §4.2) - lower bound. Unset = the preset for this template's GC class. In nt. Advanced.
  • region_end · number · optionnel
    0-based inclusive end. Unset = the whole sequence. Advanced.
  • tm_loop_max · number · optionnel
    Tm window for the loop primers LF / LB - upper bound. Unset = the preset for this template's GC class. In °C. Advanced.
  • tm_loop_min · number · optionnel
    Tm window for the loop primers LF / LB - lower bound. Unset = the preset for this template's GC class. In °C. Advanced.
  • loop_primers · boolean · optionnel
    design LF/LB as well. They are optional in LAMP and accelerate the reaction.
  • region_start · number · optionnel
    0-based inclusive start of the region to design into (LAMP designs into a stretch, not a whole plasmid). Unset = the whole sequence; pass the selection's start to scope to it. Advanced.
  • tm_inner_max · number · optionnel
    Tm window for F1c / B1c - the manual's "about 65 °C" - upper bound. Unset = the preset for this template's GC class. In °C. Advanced.
  • tm_inner_min · number · optionnel
    Tm window for F1c / B1c - the manual's "about 65 °C" - lower bound. Unset = the preset for this template's GC class. In °C. Advanced.
  • tm_outer_max · number · optionnel
    Tm window for F2 / B2 / F3 / B3 - the manual's "about 60 °C" - upper bound. Unset = the preset for this template's GC class. In °C. Advanced.
  • tm_outer_min · number · optionnel
    Tm window for F2 / B2 / F3 / B3 - the manual's "about 60 °C" - lower bound. Unset = the preset for this template's GC class. In °C. Advanced.
  • loop_span_max · number · optionnel
    5' of F2 to 5' of F1 - the portion that forms the loop (manual §2.5: 40-60) - upper bound. Unset = the preset for this template's GC class. In bp. Advanced.
  • loop_span_min · number · optionnel
    5' of F2 to 5' of F1 - the portion that forms the loop (manual §2.5: 40-60) - lower bound. Unset = the preset for this template's GC class. In bp. Advanced.
  • outer_gap_max · number · optionnel
    F3 to F2 and B3 to B2 gap. THE TWO AUTHORITIES DISAGREE here too: PrimerExplorer V5 says 0-60, the Eiken genome site 0-20 - upper bound. Unset = the preset for this template's GC class. In bp. Advanced.
  • outer_gap_min · number · optionnel
    F3 to F2 and B3 to B2 gap. THE TWO AUTHORITIES DISAGREE here too: PrimerExplorer V5 says 0-60, the Eiken genome site 0-20 - lower bound. Unset = the preset for this template's GC class. In bp. Advanced.
  • end_stability_dg · number · optionnel
    the terminal-6-base stability rule (manual §2.2: the ΔG "is -4 kcal/mol or less"). In kcal/mol. Advanced.
  • end_stability_nt · number · optionnel
    how many terminal bases the end-stability rule measures (manual §2.2: 6). In nt. Advanced.
  • amplified_span_max · number · optionnel
    F2 5' to B2 5', the amplified region. THE TWO AUTHORITIES DISAGREE: PrimerExplorer V5 says 120-160, the Eiken genome site 120-180; the default follows PrimerExplorer and this is the knob for the other reading - upper bound. Unset = the preset for this template's GC class. In bp. Advanced.
  • amplified_span_min · number · optionnel
    F2 5' to B2 5', the amplified region. THE TWO AUTHORITIES DISAGREE: PrimerExplorer V5 says 120-160, the Eiken genome site 120-180; the default follows PrimerExplorer and this is the knob for the other reading - lower bound. Unset = the preset for this template's GC class. In bp. Advanced.

  Exemple d'appel

  {"name": "design_lamp_primers", "arguments": {"_files": [], "gc_max": 1, "gc_min": 1, "_subject": {}, "max_sets": 1, "length_max": 1}}

  Exemple de retour

  {"content": [{"type": "text", "text": "…"}], "structuredContent": {"b3": "texte", "f3": "texte", "bip": "texte", "fip": "texte", "sets": "texte", "offset": 1, "setCount": 1, "constraints": "texte", "targetClass": "texte", "penaltyTerms": "texte"}}

• design_merfish_probes≈ 1915 tokens

  Design MERFISH encoding probes for the subject transcript: tile it into target regions, keep those whose G+C and melting temperature fall in their windows, that share no k-mer with an rRNA or tRNA, and whose k-mers occur in this gene's transcripts and nowhere else in the transcriptome; attach readout sequences that spell the gene's codeword, add the amplification primers, screen the whole oligo again, select probes that cover every on-bit evenly with least overlap, and drop probes complementary to one another. Each stage reports how many it kept.

  Paramètres, retour & exemple (32)

  Paramètres

  • seed · number · optionnel
    seed for the random draws in readout assignment and selection. Advanced.
  • _files · array · optionnel
    The project: record references shaped like _subject. Their records become library documents a tool names in sequences/parts/document; a trace or alignment is found by file name.
  • max_gc · number · optionnel
    highest G+C of a target region (exclusive). In %.
  • max_tm · number · optionnel
    highest melting temperature of a target region (exclusive). In °C.
  • min_gc · number · optionnel
    lowest G+C of a target region (exclusive). In %.
  • min_tm · number · optionnel
    lowest melting temperature of a target region (exclusive). In °C.
  • spacer · string · optionnel
    bases between each readout and the target. Advanced.
  • trials · number · optionnel
    selection runs; the one with the most even on-bit coverage is kept. Advanced.
  • barcode · string · optionnel
    the gene's codeword, one 0 or 1 per bit, 1 where the bit is on.
  • rtrna_k · number · optionnel
    k-mer length of the rRNA/tRNA screen. Advanced.
  • _subject · object · optionnel
    The record to act on: exactly one of sequence, accession (+source), sample (an id from list_samples) or file ({name, text} or {name, base64}); record_index picks one record of several.
  • probe_nm · number · optionnel
    concentration of each probe. In nM. Advanced.
  • readouts · string · optionnel
    the readout sequences as FASTA, one per bit, in bit order.
  • formamide · number · optionnel
    formamide in the hybridization buffer. In %. Advanced.
  • sodium_mm · number · optionnel
    monovalent salt of the hybridization buffer. In mM. Advanced.
  • t7_length · number · optionnel
    bases of the reverse primer lost in in vitro transcription. In nt. Only applies when reverse_primer is set. Advanced.
  • target_id · string · optionnel
    the transcript to design for, by its FASTA id. Empty: the transcript whose sequence is the subject's. Advanced.
  • expression · string · optionnel
    expression per transcript, one 'id value' line each (FPKM or TPM). Empty: every transcript weighs 1, MERFISH_probe_design's own choice without expression data. Advanced.
  • cross_talk_k · number · optionnel
    k-mer length of the library-wide cross-hybridization screen. Advanced.
  • max_rtrna_ot · number · optionnel
    highest rRNA/tRNA off-target count to keep (exclusive); 0.5 keeps only regions with none. Advanced.
  • specificity_k · number · optionnel
    k-mer length of the specificity and readout off-target counts. Advanced.
  • target_length · number · optionnel
    length of each target region. In nt.
  • transcriptome · string · optionnel
    every transcript of the organism as FASTA (RefSeq titles name the gene in their last parentheses); the subject is found in it by sequence.
  • forward_primer · string · optionnel
    forward primer; its reverse complement ends the oligo. Only applies when reverse_primer is set. Advanced.
  • reverse_primer · string · optionnel
    reverse primer, T7 promoter at its 5' end. Empty: no primers are added. Advanced.
  • min_specificity · number · optionnel
    lowest specificity to keep (exclusive): the share of a region's k-mers found only in this gene.
  • rtrna_reference · string · optionnel
    rRNA and tRNA sequences as FASTA. An Ensembl ncRNA FASTA is filtered to those biotypes by its headers. Empty: the rRNA/tRNA screen does not run.
  • one_bit_per_probe · boolean · optionnel
    give each probe copies of a single readout. Advanced.
  • readout_assignment · string · optionnel · balanced | random
    how each probe's on-bits are drawn: balanced keeps every on-bit equally used down the transcript. Advanced.
  • readouts_per_probe · number · optionnel
    readout sequences carried by each probe, split between its two ends.
  • probes_per_transcript · number · optionnel
    probes to select.
  • max_readout_ot_increase · number · optionnel
    drop a probe whose readouts add this many expression-weighted off-target k-mers or more (the single-molecule pipeline's check). Empty: not checked. Advanced.

  Exemple d'appel

  {"name": "design_merfish_probes", "arguments": {"seed": 1, "_files": [], "max_gc": 1, "max_tm": 1, "min_gc": 1, "min_tm": 1}}

  Exemple de retour

  {"content": [{"type": "text", "text": "…"}], "structuredContent": {"probes": "texte", "report": "texte", "stages": "texte", "orderTable": "texte", "probeCount": 1, "explanation": "texte"}}

• design_multisite_primers≈ 2208 tokens

  Design QCLM (quick-change lightning multi-site) oligos: one primer per mutated site, all annealing in one reaction, with the codons drawn from an organism's usage table. A design/write.

  Paramètres, retour & exemple (39)

  Paramètres

  • k · number · optionnel
    potassium concentration. In mM. Advanced.
  • mg · number · optionnel
    magnesium concentration — the term the Owczarzy corrections are most sensitive to. In mM. Advanced.
  • na · number · optionnel
    sodium concentration the salt correction is computed for. In mM. Only applies when gc_value_set is Schildkraut_1965 or Primer3 or Ahsen_2001. Advanced.
  • cds · string · requis
    the CDS nucleotide sequence, in frame from the start codon.
  • dntp · number · optionnel
    total dNTP concentration, which chelates magnesium and so lowers the effective Mg²⁺. In mM. Advanced.
  • seed · number · optionnel
    seed for the codon draw. The same seed and the same request give the same oligos; change it to re-roll.
  • tris · number · optionnel
    Tris concentration. In mM. Only applies when gc_value_set is Schildkraut_1965 or Primer3 or Ahsen_2001. Advanced.
  • _files · array · optionnel
    The project: record references shaped like _subject. Their records become library documents a tool names in sequences/parts/document; a trace or alignment is found by file name.
  • _subject · object · optionnel
    The record to act on: exactly one of sequence, accession (+source), sample (an id from list_samples) or file ({name, text} or {name, base64}); record_index picks one record of several.
  • organism · string · optionnel · e-coli | yeast
    codon-usage table the synonymous choice is drawn from.
  • mutations · string · requis
    the substitutions, comma- or space-separated, as [WT][pos][MUT] — e.g. "E42L, E42W, K107M". Several entries at one position are ONE site delivering several aminos.
  • precision · number · optionnel
    decimal places the reported Tm is rounded to. In dp. Advanced.
  • temp_weight · number · optionnel
    score weight on Tm deviation. Advanced.
  • use_primer3 · boolean · optionnel
    apply primer3 hairpin / homodimer / heterodimer penalties. Advanced.
  • gc_value_set · string · optionnel · QuickChange | Chester_1993 | Schildkraut_1965 | Primer3 | Ahsen_2001
    which published GC-formula parameter set the melting temperature is computed under. Values: QuickChange (QuikChange (the kit manufacturer’s own formula)), Chester_1993 (Marmur-Doty (Chester & Marshak 1993)), Schildkraut_1965 (Schildkraut & Lifson 1965 (Marmur-Doty + log[Na⁺])), Primer3 (Primer3Plus product Tm (Biopython’s default set)), Ahsen_2001 (von Ahsen 2001 (accuracy against ease of use)). Advanced.
  • five_end_flank · string · optionnel
    explicit 5' context. Left empty, 60 bp is read off the open record either side of the CDS. Advanced.
  • max_gc_content · number · optionnel
    highest GC accepted. In %. Advanced.
  • min_gc_content · number · optionnel
    lowest oligo GC accepted. In %. Advanced.
  • max_primer_size · number · optionnel
    longest oligo. In nt. Advanced.
  • max_temperature · number · optionnel
    highest Tm threshold swept. In °C.
  • min_primer_size · number · optionnel
    shortest oligo. In nt. Advanced.
  • min_temperature · number · optionnel
    lowest Tm threshold the growth scan sweeps. In °C.
  • temp_range_size · number · optionnel
    width of the acceptable Tm window around the reaction temperature. In °C. Advanced.
  • three_end_flank · string · optionnel
    explicit 3' context, the partner of `five_end_flank`. Advanced.
  • gc_content_weight · number · optionnel
    score weight on GC overflow. Advanced.
  • max_five_end_size · number · optionnel
    longest 5' lead. In nt. Advanced.
  • min_five_end_size · number · optionnel
    bases between the 5' terminus and the first mutated codon, minimum. In nt. Advanced.
  • max_three_end_size · number · optionnel
    longest 3' tail. In nt. Advanced.
  • min_three_end_size · number · optionnel
    bases between the last mutated codon and the 3' terminus, minimum. In nt. Advanced.
  • primer_size_weight · number · optionnel
    score weight on oligo length deviation. Advanced.
  • temp_threshold_step · number · optionnel
    step between Tm thresholds tried. In °C. Advanced.
  • five_end_size_weight · number · optionnel
    score weight on 5'-lead length deviation. Advanced.
  • use_degeneracy_codon · boolean · optionnel
    collapse a site's codons into one IUPAC-degenerate codon (upstream's default). Off, each amino gets its own oligo.
  • three_end_size_weight · number · optionnel
    score weight on 3'-tail length deviation. Advanced.
  • non_overlapping_primers · boolean · optionnel
    forbid oligos from overlapping each other. Upstream ranks only the LAST split's solutions with this on (a reproduced bug, see the port header). Advanced.
  • mutation_coverage_weight · number · optionnel
    score weight on how many of the requested aminos the design actually delivers — upstream's dominant term. Advanced.
  • hairpin_temperature_weight · number · optionnel
    score weight on hairpin Tm. Advanced.
  • codon_usage_frequency_threshold · number · optionnel
    discard synonymous codons rarer than this fraction in the chosen organism.
  • primer_dimer_temperature_weight · number · optionnel
    score weight on dimer Tm. Advanced.

  Exemple d'appel

  {"name": "design_multisite_primers", "arguments": {"cds": "texte", "mutations": "texte"}}

  Exemple de retour

  {"content": [{"type": "text", "text": "…"}], "structuredContent": {"seed": 1, "oligos": "texte", "failureCount": 1, "fullSequence": "texte", "mutationCoverage": 1, "reactionTemperature": 1}}

• design_mutagenesis_primers≈ 1053 tokens

  Design site-directed mutagenesis (SOE-PCR/QuikChange) primers for a point change on a CDS: the ranked inner mutagenic pairs, the constant outer pair, and the single spanning primer that replaces an outer when the site sits too near a CDS end. A design/write.

  Paramètres, retour & exemple (6)

  Paramètres

  • cds · string · requis
    the CDS nucleotide sequence, in frame from the start codon.
  • _files · array · optionnel
    The project: record references shaped like _subject. Their records become library documents a tool names in sequences/parts/document; a trace or alignment is found by file name.
  • _subject · object · optionnel
    The record to act on: exactly one of sequence, accession (+source), sample (an id from list_samples) or file ({name, text} or {name, base64}); record_index picks one record of several.
  • mutation · string · requis
    the change as [WT][pos][MUT], e.g. "W140F" (1-based residue).
  • tm_model · string · optionnel · santalucia | wallace | gc:Chester_1993 | gc:QuickChange | gc:Schildkraut_1965 | gc:Wetmur_Melting_1991 | gc:Wetmur_RNA_1991 | gc:Wetmur_DNA_RNA_1991
    Tm scale the candidates are scored and ranked on. The 55-75 °C window is calibrated for SantaLucia NN; `wallace` is upstream's primer3-free fallback, kept for golden parity. Values: santalucia (SantaLucia nearest-neighbor (Biopython Tm_NN defaults)), wallace (Wallace rule (4 °C per G·C, 2 °C per A·T)), gc:Chester_1993 (GC formula: Marmur-Doty (Chester & Marshak 1993)), gc:QuickChange (GC formula: QuikChange (the kit manufacturer’s own formula)), gc:Schildkraut_1965 (GC formula: Schildkraut & Lifson 1965 (Marmur-Doty + log[Na⁺])), gc:Wetmur_Melting_1991 (GC formula: Wetmur 1991, DNA (MELTING 4.3 approximate mode)), gc:Wetmur_RNA_1991 (GC formula: Wetmur 1991, RNA), gc:Wetmur_DNA_RNA_1991 (GC formula: Wetmur 1991, RNA/DNA hybrid), gc:Primer3 (GC formula: Primer3Plus product Tm (Biopython’s default set)), gc:Ahsen_2001 (GC formula: von Ahsen 2001 (accuracy against ease of use)).
  • codon_usage_tsv · string · optionnel
    codon-usage table the mutant codon is drawn from, as a Kazusa-style TSV. Left empty it is the built-in E. coli K12 table, which is what the panel's codon picker opens on. Advanced.

  Exemple d'appel

  {"name": "design_mutagenesis_primers", "arguments": {"cds": "texte", "mutation": "texte"}}

  Exemple de retour

  {"content": [{"type": "text", "text": "…"}], "structuredContent": {"outer": "texte", "wtCodon": "texte", "edgeCase": "texte", "mutCodon": "texte", "ntChanges": 1, "candidates": "texte", "ntPosition": 1}}

• design_oligo_plate_order≈ 1184 tokens

  Lay a set of oligos out as a supplier's PLATE order sheet: one worksheet per plate, in the well order the supplier's own order form fills, with the column shape its loading direction requires. A plate order is addressed BY WELL, which a flat tube list cannot express — so this is the shape an oligo set actually gets ordered in once it outgrows a handful of tubes. With `mixed`, a forward and a reverse share one well, which is what the supplier's doubled mix-plate layouts encode. It WRITES A FILE and sends nothing: no account, no key, no network call.

  Paramètres, retour & exemple (9)

  Paramètres

  • fill · string · optionnel · rows | columns | explicit
    how the plate is loaded. It decides the FILE'S COLUMNS, not just the order: a plate filled by row or by column carries no well column at all, because the supplier derives each position from the row order. Values: rows (Rows (A1, A2, A3 …)), columns (Columns (A1, B1, C1 …)), explicit (Explicitly entered).
  • mixed · boolean · optionnel
    one well per PRIMER PAIR: `oligos` is read as forward, reverse, forward, reverse, and each plate is written as every well once carrying the forwards and again carrying the reverses.
  • names · array · requis
    a name per oligo, in the same order. A plate well is ORDERED BY NAME, so an unnamed oligo is refused rather than numbered: the label is what the supplier ships the tube under.
  • _files · array · optionnel
    The project: record references shaped like _subject. Their records become library documents a tool names in sequences/parts/document; a trace or alignment is found by file name.
  • format · number · optionnel · 96 | 384
    wells per plate. Values: 96 (96 well), 384 (384 well).
  • oligos · array · requis
    the oligos to lay out, 5'→3'. Wire them from a design run, or list them. With `mixed`, these are read in FORWARD, REVERSE order — two entries per well.
  • _subject · object · optionnel
    The record to act on: exactly one of sequence, accession (+source), sample (an id from list_samples) or file ({name, text} or {name, base64}); record_index picks one record of several.
  • plate_name · string · optionnel
    the plate's name, which becomes the worksheet's name. Several plates get ' (2)', ' (3)' appended.
  • pad_to_capacity · boolean · optionnel
    write every unused well as the supplier's blank-name, blank-sequence row rather than ending the sheet short. Advanced.

  Exemple d'appel

  {"name": "design_oligo_plate_order", "arguments": {"names": [], "oligos": []}}

  Exemple de retour

  {"content": [{"type": "text", "text": "…"}], "structuredContent": {"tsv": "texte", "sheets": "texte", "columns": "texte", "reading": "texte", "refused": "texte", "wellNote": "texte", "plateCount": 1}}

• design_overhang_set≈ 1056 tokens

  Design a high-fidelity Golden Gate overhang set of a given size against measured ligation data, optionally pinning junctions you cannot change (a fixed vector's own overhangs). The counterpart to score_overhang_fidelity: that grades a set you already have, this proposes one. The search is greedy-plus-steepest-ascent over the same golden-validated objective: real measured data, a heuristic path, no claim of finding the optimum.

  Paramètres, retour & exemple (8)

  Paramètres

  • size · number · optionnel
    how many junctions the assembly needs (parts + 1 for a circular construct, counted as junctions).
  • fixed · array · optionnel
    junctions you cannot change, such as a destination vector's own overhangs. They are never considered for replacement and are counted inside `size`.
  • _files · array · optionnel
    The project: record references shaped like _subject. Their records become library documents a tool names in sequences/parts/document; a trace or alignment is found by file name.
  • enzyme · string · optionnel
    the Type-IIS enzyme the reaction uses, which picks that enzyme's own measured matrix when one exists. Only applies when dataset is not given.
  • dataset · string · optionnel · BsaI-HFv2 | BsmBI-v2 | Esp3I | BbsI-HF | SapI | T4-01h-25C | T4-01h-37C | T4-18h-25C
    design against this measured matrix instead of the one the enzyme implies. Values: BsaI-HFv2 (BsaI-HFv2, Golden Gate cycling (4 nt)), BsmBI-v2 (BsmBI-v2, Golden Gate cycling (4 nt)), Esp3I (Esp3I, Golden Gate cycling (4 nt)), BbsI-HF (BbsI-HF, Golden Gate cycling (4 nt)), SapI (SapI, Golden Gate cycling (3 nt)), T4-01h-25C (T4 DNA ligase, 1 h at 25 C (4 nt)), T4-01h-37C (T4 DNA ligase, 1 h at 37 C (4 nt)), T4-18h-25C (T4 DNA ligase, 18 h at 25 C (4 nt)), T4-18h-37C (T4 DNA ligase, 18 h at 37 C (4 nt)).
  • _subject · object · optionnel
    The record to act on: exactly one of sequence, accession (+source), sample (an id from list_samples) or file ({name, text} or {name, base64}); record_index picks one record of several.
  • start_from · array · optionnel
    the set you already have, as a second starting point. Given one of the same size, the answer is never WORSE than it: the greedy build alone can land in its own basin and lose points against a real set. Wire `golden_gate_assemble.overhangs` here.
  • candidate_pool · number · optionnel
    how many of the strongest-annealing overhangs the search considers. Higher is a better set and a slower run. Advanced.

  Exemple d'appel

  {"name": "design_overhang_set", "arguments": {"size": 1, "fixed": [], "_files": [], "enzyme": "texte", "dataset": "BsaI-HFv2", "_subject": {}}}

  Exemple de retour

  {"content": [{"type": "text", "text": "…"}], "structuredContent": {"from": "texte", "fixed": "texte", "dataset": "texte", "percent": 1, "fidelity": 1, "overhangs": "texte"}}

• design_padlock_probes≈ 1044 tokens

  Design padlock probes for in-situ sequencing against the subject: find the two-arm targets whose melting temperature falls in a window, check each against a BLAST search for any other transcript that could be ligated across the junction, pack non-overlapping targets from the 3' end, and assemble each into its padlock with the backbone given. Without BLAST results it returns the targets to search, and says the junction check has not been run.

  Paramètres, retour & exemple (11)

  Paramètres

  • _files · array · optionnel
    The project: record references shaped like _subject. Their records become library documents a tool names in sequences/parts/document; a trace or alignment is found by file name.
  • max_tm · number · optionnel
    highest target melting temperature to accept (exclusive). In °C.
  • min_tm · number · optionnel
    lowest target melting temperature to accept (exclusive), at 0.1 µM probe, 75 mM monovalent, 10 mM divalent salt and 20% formamide. In °C.
  • barcode · string · optionnel
    the barcode read out by sequencing. Advanced.
  • _subject · object · optionnel
    The record to act on: exactly one of sequence, accession (+source), sample (an id from list_samples) or file ({name, text} or {name, base64}); record_index picks one record of several.
  • interval · number · optionnel
    fewest bases between two packed targets. In nt.
  • variants · string · optionnel
    comma-separated accessions (no version) that count as the target itself, such as its isoforms. Empty: a hit counts as the target only when its accession is in the subject's name. Only applies when blast_csv is set. Advanced.
  • blast_csv · string · optionnel
    blastn -outfmt 10 output for the targets FASTA this tool returns (run with -word_size 7 -strand plus against your transcriptome). Without it no target is checked for junction specificity.
  • arm_length · number · optionnel
    length of each target arm; the target is twice this. In nt.
  • linker_upstream · string · optionnel
    backbone sequence between the 3' arm and the barcode. Advanced.
  • linker_downstream · string · optionnel
    backbone sequence between the barcode and the 5' arm. Advanced.

  Exemple d'appel

  {"name": "design_padlock_probes", "arguments": {"_files": [], "max_tm": 1, "min_tm": 1, "barcode": "texte", "_subject": {}, "interval": 1}}

  Exemple de retour

  {"content": [{"type": "text", "text": "…"}], "structuredContent": {"packed": "texte", "padlocks": "texte", "explanation": "texte", "padlockCount": 1, "targetsFasta": "texte"}}

• design_primer_pairs≈ 2733 tokens

  The Primer Designer's own ranked search: scan the open record for primer pairs inside a product-size, Tm, length and GC window, score every candidate on Tm, dimers, hairpins, 3' stability, repeats, clamp and specificity under weights you set, and return the best N. With `task: existing`, supply one primer and it designs the mate. Emits the top pair so a downstream pcr_amplify runs on it. For a sequencing walk use design_sequencing_primers; for pydna's single-pair designer use design_primers.

  Paramètres, retour & exemple (39)

  Paramètres

  • task · string · optionnel · new | existing
    `new` ranks candidate pairs; `existing` keeps the primer you supply and designs its mate.
  • _files · array · optionnel
    The project: record references shaped like _subject. Their records become library documents a tool names in sequences/parts/document; a trace or alignment is found by file name.
  • gc_max · number · optionnel
    highest primer GC accepted. In %.
  • gc_min · number · optionnel
    lowest primer GC accepted. In %.
  • n_pairs · number · optionnel
    how many ranked pairs to return.
  • _subject · object · optionnel
    The record to act on: exactly one of sequence, accession (+source), sample (an id from list_samples) or file ({name, text} or {name, base64}); record_index picks one record of several.
  • excluded · array · optionnel
    spans no primer may sit on, as find_primer_snps' `excluded` emits them: a list of {start, end}, 0-based and end-exclusive, where start = end is an insertion between two bases. The amplicon may run across them. The panel's Avoid known SNPs. Advanced.
  • fwd_tail · string · optionnel
    5' non-annealing tail added to every forward primer (a restriction site or adapter). The footprint, and so binding and Tm, is unchanged. Advanced.
  • rev_tail · string · optionnel
    5' non-annealing tail added to every reverse primer. Advanced.
  • target_tm · number · optionnel
    the Tm each primer is scored toward. In °C.
  • weight_gc · number · optionnel
    scoring weight for the `gc` penalty (0 switches it off). Advanced.
  • weight_tm · number · optionnel
    scoring weight for the `tm` penalty (0 switches it off). Advanced.
  • conditions · object · optionnel
    salt, magnesium, dNTP and oligo concentrations plus the salt-correction method the Tm window is measured in. Left unset it is filled from your reaction-conditions settings, as the panel's are. Advanced.
  • region_end · number · optionnel
    0-based inclusive end of the region to design within. Advanced.
  • target_end · number · optionnel
    0-based inclusive end of the target. Advanced.
  • weight_end3 · number · optionnel
    scoring weight for the `end3` penalty (0 switches it off). Advanced.
  • region_start · number · optionnel
    0-based inclusive start of the region to design within. Unset = the whole template. Advanced.
  • target_start · number · optionnel
    0-based inclusive start of a target the amplicon must flank, with no primer on it. Advanced.
  • tm_window_max · number · optionnel
    highest primer Tm accepted at all. In °C.
  • tm_window_min · number · optionnel
    lowest primer Tm accepted at all. In °C.
  • weight_length · number · optionnel
    scoring weight for the `length` penalty (0 switches it off). Advanced.
  • weight_poly_x · number · optionnel
    scoring weight for the `polyX` penalty (0 switches it off). Advanced.
  • weight_hairpin · number · optionnel
    scoring weight for the `hairpin` penalty (0 switches it off). Advanced.
  • weight_tm_pair · number · optionnel
    scoring weight for the `tmPair` penalty (0 switches it off). Advanced.
  • weight_gc_clamp · number · optionnel
    scoring weight for the `gcClamp` penalty (0 switches it off). Advanced.
  • weight_self_end · number · optionnel
    scoring weight for the `selfEnd` penalty (0 switches it off). Advanced.
  • existing_forward · string · optionnel
    with `task: existing`, the forward primer to keep. Only applies when task is existing.
  • existing_reverse · string · optionnel
    with `task: existing`, the reverse primer to keep. Only applies when task is existing.
  • product_size_max · number · optionnel
    longest acceptable amplicon. In bp.
  • product_size_min · number · optionnel
    shortest acceptable amplicon. In bp.
  • weight_cross_end · number · optionnel
    scoring weight for the `crossEnd` penalty (0 switches it off). Advanced.
  • weight_di_repeat · number · optionnel
    scoring weight for the `diRepeat` penalty (0 switches it off). Advanced.
  • primer_length_max · number · optionnel
    longest primer. In nt.
  • primer_length_min · number · optionnel
    shortest primer. In nt.
  • weight_mispriming · number · optionnel
    scoring weight for the `mispriming` penalty (0 switches it off). Advanced.
  • weight_self_dimer · number · optionnel
    scoring weight for the `selfDimer` penalty (0 switches it off). Advanced.
  • mispriming_library · string · optionnel · none | human | rodent | drosophila
    a Primer3 repeat library to screen every primer against. `none` skips the screen. Advanced.
  • weight_cross_dimer · number · optionnel
    scoring weight for the `crossDimer` penalty (0 switches it off). Advanced.
  • weight_specificity · number · optionnel
    scoring weight for the `specificity` penalty (0 switches it off). Advanced.

  Exemple d'appel

  {"name": "design_primer_pairs", "arguments": {"task": "new", "_files": [], "gc_max": 1, "gc_min": 1, "n_pairs": 1, "_subject": {}}}

  Exemple de retour

  {"content": [{"type": "text", "text": "…"}], "structuredContent": {"ta": 1, "pairs": "texte", "forward": "texte", "reverse": "texte", "pairCount": 1, "shortfall": "texte", "productLen": 1}}

• design_primers≈ 1455 tokens

  Design a forward + reverse primer pair to amplify the subject (pydna `primer_design`), with Tm, Ta and suggested Taq/Phusion cycling programs. Emits both primers so a downstream pcr_amplify runs on them — the design→PCR→gel loop.

  Paramètres, retour & exemple (7)

  Paramètres

  • limit · number · optionnel
    minimum primer length (pydna `limit`). In bp. Advanced.
  • _files · array · optionnel
    The project: record references shaped like _subject. Their records become library documents a tool names in sequences/parts/document; a trace or alignment is found by file name.
  • _subject · object · optionnel
    The record to act on: exactly one of sequence, accession (+source), sample (an id from list_samples) or file ({name, text} or {name, base64}); record_index picks one record of several.
  • target_tm · number · optionnel
    target melting temperature (pydna default 55). In °C.
  • conditions · object · optionnel
    salt, magnesium, dNTP and oligo concentrations plus the salt-correction method and any additives the target Tm is measured in. Left unset it is filled from your reaction-conditions settings, and falls back to the nearest-neighbour defaults when there are none. Advanced.
  • forward_primer · string · optionnel
    supply one primer to design only its mate. Advanced.
  • reverse_primer · string · optionnel
    supply one primer to design only its mate. Advanced.

  Exemple d'appel

  {"name": "design_primers", "arguments": {"limit": 1, "_files": [], "_subject": {}, "target_tm": 1, "conditions": {}, "forward_primer": "texte"}}

  Exemple de retour

  {"content": [{"type": "text", "text": "…"}], "structuredContent": {"ta": 1, "forward": "texte", "program": "texte", "reverse": "texte", "forwardTm": 1, "productTm": 1, "reverseTm": 1, "productLen": 1}}

• design_qpcr_assay≈ 2750 tokens

  Design qPCR assays over the subject — primer pair plus hydrolysis probe, ranked by penalty, with amplicon size/GC, per-oligo Tm and whether both primers bind a single site.

  Paramètres, retour & exemple (29)

  Paramètres

  • _files · array · optionnel
    The project: record references shaped like _subject. Their records become library documents a tool names in sequences/parts/document; a trace or alignment is found by file name.
  • _subject · object · optionnel
    The record to act on: exactly one of sequence, accession (+source), sample (an id from list_samples) or file ({name, text} or {name, base64}); record_index picks one record of several.
  • conditions · object · optionnel
    salt, magnesium, dNTP and oligo concentrations plus the salt-correction method and any DMSO or formamide that every Tm in this design is measured in. Left unset it is filled from your reaction-conditions settings, and falls back to the nearest-neighbour defaults when there are none. Advanced.
  • max_poly_x · number · optionnel
    longest run of one base allowed in any oligo (primer3's POLY_X). A long run mispairs by slipping, and for a TaqMan probe a run of four or more Gs quenches the reporter. In nt. Advanced.
  • region_end · number · optionnel
    0-based inclusive end. Unset = the whole sequence. Advanced.
  • max_results · number · optionnel
    how many assays to return, best penalty first.
  • amplicon_max · number · optionnel
    longest acceptable amplicon - qPCR amplicons are short on purpose, because a short product amplifies efficiently enough for the exponential phase to be clean. In bp.
  • amplicon_min · number · optionnel
    shortest acceptable amplicon. In bp.
  • probe_max_gc · number · optionnel
    highest acceptable probe GC content. In %. Advanced.
  • probe_max_tm · number · optionnel
    probes above this Tm are rejected outright. In °C. Advanced.
  • probe_min_gc · number · optionnel
    lowest acceptable probe GC content. In %. Advanced.
  • probe_min_tm · number · optionnel
    probes below this Tm are rejected outright. In °C. Advanced.
  • probe_tm_opt · number · optionnel
    target probe Tm - conventionally ~10 °C above the primers, so the probe is bound before extension reaches it. In °C.
  • region_start · number · optionnel
    0-based inclusive start of the region to design in. Unset = the whole sequence; pass the selection's start to scope to it. Advanced.
  • primer_max_gc · number · optionnel
    highest acceptable primer GC content. In %. Advanced.
  • primer_max_tm · number · optionnel
    primers above this Tm are rejected outright. In °C. Advanced.
  • primer_min_gc · number · optionnel
    lowest acceptable primer GC content. In %. Advanced.
  • primer_min_tm · number · optionnel
    primers below this Tm are rejected outright, not merely penalised. In °C. Advanced.
  • primer_tm_opt · number · optionnel
    target primer Tm; the penalty ranks candidates by their distance from it. In °C.
  • probe_chemistry · string · optionnel · dna | lna
    what the hydrolysis probe is made of. `dna` is unmodified DNA; `lna` locks the bases named by `probe_locked_positions`, which raises the probe Tm and is how a short probe reaches the TaqMan offset over its primers. MGB and Scorpion chemistries are not offered: neither has a published nearest-neighbour parameter set to compute a Tm from.
  • structure_check · boolean · optionnel
    run the `thal` secondary-structure check on the RETURNED assays: hairpin and cross-dimer melting temperatures for all three oligos and every pairing between them. On by default, because a qPCR assay that dimerises is the commonest design failure and penalty ranking alone will happily put one first. Off returns null structures and is measurably faster - the check is a dynamic-programming alignment per oligo pair. Advanced.
  • probe_max_length · number · optionnel
    longest probe considered. In nt. Advanced.
  • probe_min_length · number · optionnel
    shortest probe considered. In nt. Advanced.
  • probe_opt_length · number · optionnel
    probe length the penalty prefers. In nt. Advanced.
  • primer_max_length · number · optionnel
    longest primer considered; primer3's own ceiling is 36. In nt. Advanced.
  • primer_min_length · number · optionnel
    shortest primer considered. In nt. Advanced.
  • primer_opt_length · number · optionnel
    primer length the penalty prefers. In nt. Advanced.
  • probe_tm_offset_min · number · optionnel
    how many °C the probe Tm must exceed the MEAN primer Tm. TaqMan guidance is 8-10; below that the probe can melt off before it is cleaved. In °C.
  • probe_locked_positions · string · optionnel
    which bases to lock, 1-based from the probe's 5′ end, e.g. `3, 6, 9`. Read only when `probe_chemistry` is `lna`. Positions must be interior to the SHORTEST probe the search will try and never adjacent, because McTigue et al. (2004) measured one locked base per nearest neighbour and none at a duplex end - a position that breaks either rule is refused by name rather than silently dropped. Only applies when probe_chemistry is lna.

  Exemple d'appel

  {"name": "design_qpcr_assay", "arguments": {"_files": [], "_subject": {}, "conditions": {}, "max_poly_x": 1, "region_end": 1, "max_results": 1}}

  Exemple de retour

  {"content": [{"type": "text", "text": "…"}], "structuredContent": {"best": "texte", "count": 1, "probe": "texte", "assays": "texte", "offset": 1, "forward": "texte", "reverse": "texte", "conditions": "texte", "probe_ordered": "texte"}}

• design_rbs≈ 740 tokens

  Design a 5'UTR (Shine-Dalgarno + spacer) in front of a CDS to hit a target translation-initiation strength (SC-08 engine, Turner-2004 folding).

  Paramètres, retour & exemple (5)

  Paramètres

  • cds · string · optionnel
    the CDS starting at its start codon; unset = the open record's sequence.
  • _files · array · optionnel
    The project: record references shaped like _subject. Their records become library documents a tool names in sequences/parts/document; a trace or alignment is found by file name.
  • _subject · object · optionnel
    The record to act on: exactly one of sequence, accession (+source), sample (an id from list_samples) or file ({name, text} or {name, base64}); record_index picks one record of several.
  • upstream · string · optionnel
    upstream context 5' of the UTR (engine default when unset). Advanced.
  • target_strength · number · requis
    target relative strength, on the model's own scale — 1 is as strong as its reference site, and real sites do score above it.

  Exemple d'appel

  {"name": "design_rbs", "arguments": {"target_strength": 1}}

  Exemple de retour

  {"content": [{"type": "text", "text": "…"}], "structuredContent": {"sd": "texte", "utr": "texte", "full": "texte", "dgTotal": 1, "spacing": 1, "onTarget": true, "relStrength": 1, "achievableMax": 1, "achievableMin": 1}}

• design_saturation_primers≈ 2942 tokens

  Design site-saturation mutagenesis (SSM) primers: one overlapping forward/reverse pair per site, each carrying a degenerate codon, sharing ONE reaction-level overlap and 3' temperature so every site amplifies in the same tube (both of Mutation Maker's solvers: fast approximation by default, exhaustive search on request). Every Tm is Biopython's `Tm_NN` over the Allawi & SantaLucia 1997 nearest-neighbour table (`DNA_NN3`, upstream's own), under the salt correction and buffer below. A design/write.

  Paramètres, retour & exemple (47)

  Paramètres

  • k · number · optionnel
    potassium concentration. In mM. Advanced.
  • mg · number · optionnel
    magnesium concentration — the term the Owczarzy corrections are most sensitive to. In mM. Advanced.
  • na · number · optionnel
    sodium concentration the salt correction is computed for. In mM. Advanced.
  • cds · string · requis
    the CDS nucleotide sequence, in frame from the start codon (length must be a multiple of 3).
  • dntp · number · optionnel
    total dNTP concentration, which chelates magnesium and so lowers the effective Mg²⁺. In mM. Advanced.
  • tris · number · optionnel
    Tris concentration. In mM. Advanced.
  • dnac1 · number · optionnel
    the higher-concentration strand (the primer, in a large excess). In nM. Advanced.
  • dnac2 · number · optionnel
    the lower-concentration strand (the template). In nM. Advanced.
  • sites · string · requis
    the saturation sites, comma- or space-separated, as [WT][pos]X — e.g. "V2X, K107X". 1-based residue positions.
  • _files · array · optionnel
    The project: record references shaped like _subject. Their records become library documents a tool names in sequences/parts/document; a trace or alignment is found by file name.
  • solver · string · optionnel · fast | exhaustive
    which of Mutation Maker's two solvers designs the pairs. `fast` grows one candidate per site per temperature combination (upstream's own default, milliseconds). `exhaustive` enumerates every primer of every allowed length at every allowed start and scores every geometrically valid pair — hundreds of thousands per site, seconds rather than milliseconds, and it reports what it searched. Values: fast (Fast approximation), exhaustive (Exhaustive search).
  • _subject · object · optionnel
    The record to act on: exactly one of sequence, accession (+source), sample (an id from list_samples) or file ({name, text} or {name, base64}); record_index picks one record of several.
  • precision · number · optionnel
    decimal places the reported Tm is rounded to. In dp. Advanced.
  • oligo_prefix · string · optionnel
    prefix for the designed oligo names. Advanced.
  • five_end_flank · string · optionnel
    explicit 5' flanking sequence — only for a free-standing gene with no plasmid open, and then the 3' flank is required too. Advanced.
  • forward_primer · string · optionnel
    5' flanking primer, 5'→3'. Left empty, it is read off the open plasmid 56 bp either side of the CDS (22 nt, and only when it occurs there exactly once).
  • max_gc_content · number · optionnel
    highest GC accepted. In %. Advanced.
  • min_gc_content · number · optionnel
    lowest primer GC accepted before a primer is flagged out of range. In %. Advanced.
  • reverse_primer · string · optionnel
    3' flanking primer, 5'→3' on its own strand. Left empty, it is read off the open plasmid 56 bp either side of the CDS (22 nt, and only when it occurs there exactly once).
  • max_primer_size · number · optionnel
    longest whole primer. In nt. Advanced.
  • min_primer_size · number · optionnel
    shortest whole primer. In nt. Advanced.
  • salt_correction · string · optionnel · No | Schildkraut_1965 | Wetmur_1991 | SantaLucia_1996 | SantaLucia_1998 | SantaLucia_DeltaS_1998 | Owczarzy_2004 | Owczarzy_2008
    salt-correction method, in Biopython's `saltcorr` order. Values: No (None), Schildkraut_1965 (Schildkraut & Lifson 1965 (16.6 · log[Na⁺])), Wetmur_1991 (Wetmur 1991 (16.6 · log[Na⁺/(1 + 0.7 · Na⁺)])), SantaLucia_1996 (SantaLucia 1996 (12.5 · log[Na⁺])), SantaLucia_1998 (SantaLucia 1998 (11.7 · log[Na⁺])), SantaLucia_DeltaS_1998 (SantaLucia 1998, entropy (corrects ΔS, not Tm)), Owczarzy_2004 (Owczarzy 2004 (GC-dependent, corrects 1/Tm)), Owczarzy_2008 (Owczarzy 2008 (Mg²⁺ decision tree, dNTP-corrected)). Advanced.
  • three_end_flank · string · optionnel
    explicit 3' flanking sequence, the partner of `five_end_flank`. Advanced.
  • degenerate_codon · string · optionnel
    the degenerate codon installed at every site (NNK is the common 32-codon choice).
  • max_overlap_size · number · optionnel
    longest overlap. Upstream's scan stops two short of this (a reproduced quirk, see the port header). In nt. Advanced.
  • min_overlap_size · number · optionnel
    shortest shared overlap. In nt. Advanced.
  • gc_content_weight · number · optionnel
    score weight on GC overflow. Upstream's default is 0, and its GC term counts G twice and never counts C (a reproduced bug, see the port header) — raising this weight makes that quirk observable. Advanced.
  • max_five_end_size · number · optionnel
    longest 5' arm before the mutated codon. In nt. Only applies when solver is exhaustive. Advanced.
  • min_five_end_size · number · optionnel
    shortest 5' arm before the mutated codon. In nt. Advanced.
  • max_three_end_size · number · optionnel
    longest 3' arm beyond the mutated codon. Bounds the search area and discards candidates whose 3' arm overruns it. In nt. Only applies when solver is exhaustive. Advanced.
  • min_three_end_size · number · optionnel
    shortest 3' arm beyond the mutated codon. In nt. Advanced.
  • overlap_temp_range · number · optionnel
    width of the overlap Tm window. In °C. Advanced.
  • overlap_temp_weight · number · optionnel
    score weight on overlap Tm deviation. Advanced.
  • three_end_temp_range · number · optionnel
    width of the 3'-end Tm window scanned around each candidate temperature. In °C. Advanced.
  • three_end_size_weight · number · optionnel
    score weight on 3'-end length deviation. Advanced.
  • three_end_temp_weight · number · optionnel
    score weight on 3'-end Tm deviation. Advanced.
  • max_overlap_temperature · number · optionnel
    highest overlap Tm allowed. In °C.
  • min_overlap_temperature · number · optionnel
    lowest overlap Tm the reaction may settle on. In °C.
  • overlap_temp_range_step · number · optionnel
    step between overlap temperatures tried. In °C. Advanced.
  • exclude_flanking_primers · boolean · optionnel
    take the 3' Tm window from the explicit min/max above instead of from the flanking pair's own Tm. Advanced.
  • compute_hairpin_homodimer · boolean · optionnel
    add the hairpin/homodimer/heterodimer penalty to the score (roughly doubles the run; off upstream). Advanced.
  • max_three_end_temperature · number · optionnel
    highest 3'-end Tm allowed. In °C.
  • min_three_end_temperature · number · optionnel
    lowest 3'-end Tm (used when `exclude_flanking_primers` is on; otherwise the window comes from the flanking pair). In °C. Only applies when exclude_flanking_primers is true.
  • three_end_temp_range_step · number · optionnel
    step between 3'-end temperatures tried. In °C. Advanced.
  • hairpin_temperature_weight · number · optionnel
    score weight on hairpin Tm. Only applies when compute_hairpin_homodimer is true. Advanced.
  • primer_dimer_temperature_weight · number · optionnel
    score weight on homo/heterodimer Tm. Only applies when compute_hairpin_homodimer is true. Advanced.
  • separate_forward_reverse_temperatures · boolean · optionnel
    optimise the forward and reverse 3' temperatures independently. Advanced.

  Exemple d'appel

  {"name": "design_saturation_primers", "arguments": {"cds": "texte", "sites": "texte"}}

  Exemple de retour

  {"content": [{"type": "text", "text": "…"}], "structuredContent": {"pairs": "texte", "search": "texte", "siteCount": 1, "foundCount": 1, "fullSequence": "texte", "forwardTemperature": 1, "overlapTemperature": 1, "reverseTemperature": 1}}

• design_sequencing_primers≈ 1216 tokens

  Design a WALK of sequencing primers that reads a whole region, not one pair: tiled reads with confirmed overlap, on both strands by default, plus the coverage the walk actually achieves and any stretch it cannot reach. This is the 'how do I read all 6 kb of this construct' question, which a single pair does not answer. Read length and dead zone default to a named facility's published figures (MSU RTSF, ABI 3730XL) rather than to round numbers.

  Paramètres, retour & exemple (10)

  Paramètres

  • _files · array · optionnel
    The project: record references shaped like _subject. Their records become library documents a tool names in sequences/parts/document; a trace or alignment is found by file name.
  • overlap · number · optionnel
    confirmed overlap required between consecutive reads on one strand. Overlap is what turns abutting reads into a contig. Default 100 has NO published source and is a judgement, which is why it is stated rather than dressed as a figure. In bp.
  • _subject · object · optionnel
    The record to act on: exactly one of sequence, accession (+source), sample (an id from list_samples) or file ({name, text} or {name, base64}); record_index picks one record of several.
  • dead_zone · number · optionnel
    bases at the start of a read that are not trustworthy. Default 35 is the LONGEST the same source warns about (it says the first 25-35 bases are poor), so an untouched walk is the cautious reading in both directions. In bp. Advanced.
  • target_tm · number · optionnel
    target melting temperature for each primer in the walk. In °C. Advanced.
  • min_length · number · optionnel
    shortest acceptable primer. In bp. Advanced.
  • region_end · number · optionnel
    0-based inclusive end of the region to read. Unset = the whole template. Advanced.
  • read_length · number · optionnel
    usable bases per read, AFTER the dead zone. Default 800 is the shortest read MSU RTSF Genomics Core, Sanger Sequencing Best and Worst Practices (2024-04-25), ABI 3730XL promises (it quotes 800-900), which is the cautious end of a published range rather than a round number. In bp.
  • both_strands · boolean · optionnel
    read every base from both directions - what a sequencing facility means by double-stranded coverage, and the standard for anything deposited or published.
  • region_start · number · optionnel
    0-based inclusive start of the region to read. Unset = the whole template. Advanced.

  Exemple d'appel

  {"name": "design_sequencing_primers", "arguments": {"_files": [], "overlap": 1, "_subject": {}, "dead_zone": 1, "target_tm": 1, "min_length": 1}}

  Exemple de retour

  {"content": [{"type": "text", "text": "…"}], "structuredContent": {"gaps": "texte", "used": "texte", "reads": "texte", "primers": "texte", "skipped": "texte", "complete": true, "coverage": "texte", "authority": "texte", "readCount": 1, "doubleStranded": true, "singleStranded": "texte"}}

• design_split_sites≈ 1564 tokens

  Decide where to CUT one sequence into Golden Gate fragments, optimising the split positions and the overhangs they create together. Where design_overhang_set proposes junctions for parts you already have, this fragments a sequence you are about to order: it searches every legal arrangement of fragments in your length window and ranks them by the measured ligation efficiency and fidelity of the overhangs each arrangement produces. Ported from OOGGA (Mukundan & Madhusudhan 2025) and scored against the same Potapov 2018 T4 ligase data the fidelity tools use.

  Paramètres, retour & exemple (14)

  Paramètres

  • _files · array · optionnel
    The project: record references shaped like _subject. Their records become library documents a tool names in sequences/parts/document; a trace or alignment is found by file name.
  • traces · number · optionnel
    how many ranked alternatives to return. The best arrangement is rarely the only acceptable one, and the runner-up often avoids a site you care about.
  • dataset · string · optionnel · BsaI-HFv2 | BsmBI-v2 | Esp3I | BbsI-HF | SapI | T4-01h-25C | T4-01h-37C | T4-18h-25C
    the measured ligation matrix to score against. OOGGA's own published choice is the T4 18 h 37 C set. Values: BsaI-HFv2 (BsaI-HFv2, Golden Gate cycling (4 nt)), BsmBI-v2 (BsmBI-v2, Golden Gate cycling (4 nt)), Esp3I (Esp3I, Golden Gate cycling (4 nt)), BbsI-HF (BbsI-HF, Golden Gate cycling (4 nt)), SapI (SapI, Golden Gate cycling (3 nt)), T4-01h-25C (T4 DNA ligase, 1 h at 25 C (4 nt)), T4-01h-37C (T4 DNA ligase, 1 h at 37 C (4 nt)), T4-18h-25C (T4 DNA ligase, 18 h at 25 C (4 nt)), T4-18h-37C (T4 DNA ligase, 18 h at 37 C (4 nt)). Advanced.
  • _subject · object · optionnel
    The record to act on: exactly one of sequence, accession (+source), sample (an id from list_samples) or file ({name, text} or {name, base64}); record_index picks one record of several.
  • sequence · string · optionnel
    the sequence to fragment, in one piece. Leave it empty to fragment the open record.
  • fragments · number · optionnel
    pin the number of fragments instead of letting the search choose. Leave empty to take whatever the length window allows.
  • exclude_to · number · optionnel
    end of that span, exclusive. Only applies when exclude_from is set. Advanced.
  • max_length · number · optionnel
    longest allowed fragment, in bases — the vendor's upper limit, or the length you can sequence in one read.
  • min_length · number · optionnel
    shortest allowed fragment, in bases — usually what your synthesis vendor will accept.
  • exclude_from · number · optionnel
    start of a span no cut may fall in — a feature you need kept intact. Use with exclude_to. Advanced.
  • alien_overhangs · array · optionnel
    junctions already committed elsewhere in the assembly (a fixed vector's own ends), which this set must not collide with. Advanced.
  • fidelity_weight · number · optionnel
    exponent on the running FIDELITY — raise it to favour junctions that ligate to the right partner rather than a mismatched one. Advanced.
  • efficiency_weight · number · optionnel
    exponent on the running ligation EFFICIENCY — raise it to favour junctions that ligate readily. Efficiency and fidelity are different failure modes: a junction can ligate eagerly and promiscuously. Advanced.
  • max_overhang_identity · number · optionnel
    most positions two overhangs in the set may share before they are treated as confusable. Lower is stricter and rules out more arrangements. Advanced.

  Exemple d'appel

  {"name": "design_split_sites", "arguments": {"_files": [], "traces": 1, "dataset": "BsaI-HFv2", "_subject": {}, "sequence": "texte", "fragments": 1}}

  Exemple de retour

  {"content": [{"type": "text", "text": "…"}], "structuredContent": {"score": 1, "breaks": "texte", "report": "texte", "dataset": "texte", "fragments": "texte", "overhangs": "texte", "candidates": 1, "alternatives": "texte", "net_fidelity": 1, "fragment_count": 1, "net_efficiency": 1}}

• design_xenium_probes≈ 1335 tokens

  Design Xenium custom-panel padlock targets on the subject transcript to 10x Genomics' published rules (CG000683): two 20 nt arms whose primer3 melting temperatures fall in their windows, a ligation-junction dinucleotide the Xenium ligase accepts, no run of five G in the probe, at least four mismatches across both arms to every other transcript in a BLAST search, and probes at least 10 bp apart. Without BLAST results it returns the targets to search and says the off-target check has not been run.

  Paramètres, retour & exemple (16)

  Paramètres

  • _files · array · optionnel
    The project: record references shaped like _subject. Their records become library documents a tool names in sequences/parts/document; a trace or alignment is found by file name.
  • spacing · number · optionnel
    fewest bases between two kept targets. In bp.
  • tm_rule · string · optionnel · either | full | arms | both
    which melting temperatures must fall in their windows. 10x: the full length between 68 and 82 °C or each arm between 50 and 70 °C.
  • _subject · object · optionnel
    The record to act on: exactly one of sequence, accession (+source), sample (an id from list_samples) or file ({name, text} or {name, base64}); record_index picks one record of several.
  • blast_csv · string · optionnel
    blastn -outfmt 10 output for the targets FASTA this tool returns, searched against the transcriptome (not the genome) with -word_size 7 -strand plus. Without it no target is checked for off-target homology.
  • junctions · string · optionnel · preferred | preferred and neutral | any
    ligation-junction dinucleotides to accept, from 10x's empirical ligase preferences; 10x strongly recommends avoiding the nonpreferred four.
  • max_g_run · number · optionnel
    longest run of G the probe may carry; 10x: avoid five or more. Advanced.
  • arm_length · number · optionnel
    length of each arm; the target is twice this. 10x's arms are 20 nt, shorter only for a short target whose Tm stays in range. In nt. Advanced.
  • max_arm_tm · number · optionnel
    highest Tm of each arm (inclusive). In °C.
  • min_arm_tm · number · optionnel
    lowest Tm of each arm (inclusive). In °C.
  • prefer_cds · boolean · optionnel
    rank targets inside the subject's CDS feature before the untranslated regions, as 10x advises where possible.
  • max_full_tm · number · optionnel
    highest Tm of the whole target (inclusive). In °C.
  • min_full_tm · number · optionnel
    lowest Tm of the whole target (inclusive). In °C.
  • min_mismatches · number · optionnel
    fewest mismatches across both arms an off-target hit must carry for the target to be kept; gaps and unaligned ends count. Only applies when blast_csv is set.
  • gene_accessions · string · optionnel
    comma-separated accessions (no version) that are this gene, its isoforms included: hits to them are not off-targets. Empty: the subject's name. Only applies when blast_csv is set.
  • probes_per_gene · number · optionnel
    targets to keep; 10x's predesigned panels use eight per gene.

  Exemple d'appel

  {"name": "design_xenium_probes", "arguments": {"_files": [], "spacing": 1, "tm_rule": "either", "_subject": {}, "blast_csv": "texte", "junctions": "preferred"}}

  Exemple de retour

  {"content": [{"type": "text", "text": "…"}], "structuredContent": {"probes": "texte", "stages": "texte", "probeCount": 1, "explanation": "texte", "targetsFasta": "texte"}}

• detect_trace_indel≈ 982 tokens

  Ask whether a Sanger trace splits into TWO READS OF DIFFERENT LENGTH, which is what a heterozygous insertion or deletion does: clean up to the indel, then a superposition of two sequences offset by its length. This is not mixed-base calling — that asks whether two BASES sit at one position and is blind to a length difference. Emits where the split starts, how long it is, and the two allele sequences the trace deconvolves into, so a pipeline can gate on the answer or carry either allele onward.

  Paramètres, retour & exemple (6)

  Paramètres

  • table · string · optionnel · 3700pop5 | 3700pop6 | 3100pop6 | 3730pop7
    the instrument and polymer the quality scale was calibrated on. There is no universal default: a base scores differently under a different table, and the detector gates on a quality JUMP.
  • _files · array · optionnel
    The project: record references shaped like _subject. Their records become library documents a tool names in sequences/parts/document; a trace or alignment is found by file name.
  • _subject · object · optionnel
    The record to act on: exactly one of sequence, accession (+source), sample (an id from list_samples) or file ({name, text} or {name, base64}); record_index picks one record of several.
  • document · string · optionnel
    which trace file to read: its name (`read_F.ab1`) or its project file id. LEAVE IT EMPTY to run on the chromatogram tab that is open, in which case the answer also appears in the rail. A file id is project-specific, so a template ships this unset.
  • breakpoint_scan · number · optionnel
    skip the search and measure the indel at this scan position on the x axis. -1 searches for it.
  • quality_value_reading · string · optionnel · corrected | upstream
    corrected = read the quality values as TraceTuner's own header declares them, which is the only reading that can detect anything; upstream = reproduce the program as shipped, whose detector never fires.

  Exemple d'appel

  {"name": "detect_trace_indel", "arguments": {"table": "3700pop5", "_files": [], "_subject": {}, "document": "texte", "breakpoint_scan": 1, "quality_value_reading": "corrected"}}

  Exemple de retour

  {"content": [{"type": "text", "text": "…"}], "structuredContent": {"found": true, "report": "texte", "longAllele": "texte", "qualityJump": 1, "shortAllele": "texte", "sizeInBases": 1, "startsAtBase": 1}}

• differential_expression≈ 2947 tokens

  Differential expression from raw RNA-seq read counts, by one of the three standard count models. DESeq2 (Love, Huber & Anders 2014): median-of-ratios size factors, negative-binomial GLM with empirical-Bayes shrunken dispersions, Wald or likelihood-ratio test, Cook's-distance outlier handling, independent filtering, optional LFC shrinkage. edgeR quasi-likelihood (Chen et al. 2025): filterByExpr, TMM normalization, a negative-binomial GLM with bias-adjusted QL dispersions squeezed toward an abundance trend, QL F-test. limma-voom (Law et al. 2014): filterByExpr, TMM, log-CPM with mean-variance precision weights, weighted linear models, moderated t. Takes a gene-by-sample count table and a sample table with the design's variables. Every gene of every validated fit is bit-identical to DESeq2 1.52.0, edgeR 4.10.6 and limma 3.68.5 running in R. Hands its significant genes, tested genes and ranked list on for gene-set enrichment.

  Paramètres, retour & exemple (25)

  Paramètres

  • name · string · optionnel
    one fitted coefficient to report, by its DESeq2 name (e.g. 'condition_treated_vs_untreated') or its model-matrix column ('conditiontreated'); empty is the last.
  • test · string · optionnel · Wald | LRT
    Wald: one coefficient or contrast. LRT: the full design against `reduced`, testing every removed term at once. Only applies when method is DESeq2.
  • alpha · number · optionnel
    the target FDR: the summary counts genes below this adjusted p, and DESeq2's independent filtering maximizes rejections at it.
  • _files · array · optionnel
    The project: record references shaped like _subject. Their records become library documents a tool names in sequences/parts/document; a trace or alignment is found by file name.
  • counts · string · requis
    raw read counts (never normalized values or TPM): genes in rows with the gene ID first, samples in columns, tab- or comma-separated, a header row naming the samples.
  • design · string · optionnel
    the design formula over the sample table's columns, the variable of interest last (e.g. '~ batch + condition').
  • method · string · optionnel · DESeq2 | edgeR-QL | limma-voom
    the count model: DESeq2 (negative binomial, Wald or LRT), edgeR-QL (negative binomial with quasi-likelihood F-test) or limma-voom (precision-weighted linear model on log-CPM, moderated t).
  • sfType · string · optionnel · ratio | poscounts
    size factors: median of ratios over genes with no zero (ratio), or with zeros allowed (poscounts, for sparse data). Only applies when method is DESeq2.
  • shrink · string · optionnel · none | normal | apeglm | ashr
    shrink the reported coefficient's log2 fold changes toward zero where the counts cannot support them (DESeq2 lfcShrink), for ranking and plotting by effect size; p-values stay the unshrunken test's. apeglm: adaptive Cauchy prior, posterior mode. ashr: mixture-of-normals prior, posterior mean. normal: DESeq2's original zero-centred Normal prior (Wald only). Only applies when method is DESeq2.
  • fitType · string · optionnel · parametric | mean
    the dispersion trend: parametric (asymptDisp + extraPois / mean, DESeq2's default) or the mean of gene-wise estimates. Only applies when method is DESeq2.
  • reduced · string · optionnel
    the reduced design for the likelihood-ratio test. Only applies when method is DESeq2.
  • samples · string · requis
    the sample table: a header row, then one row per sample with its name (as in the count table's header) first and the design's variables after; the run uses this table's sample order.
  • _subject · object · optionnel
    The record to act on: exactly one of sequence, accession (+source), sample (an id from list_samples) or file ({name, text} or {name, base64}); record_index picks one record of several.
  • contrast · string · optionnel
    'factor, numerator, denominator': the log2 fold change of numerator over denominator. Empty is the design's last coefficient. Under edgeR and voom the denominator must be the factor's reference level.
  • minCount · number · optionnel
    filterByExpr: the count, at the median library size, a gene needs in the smallest group's worth of samples (taken as CPM). Only applies when method is edgeR-QL or limma-voom.
  • reference · string · optionnel
    reference level per factor, 'variable=level' separated by commas; a factor not named takes its alphabetically first level, as R does.
  • cooksCutoff · number · optionnel
    the Cook's distance cutoff; empty is DESeq2's F(0.99; p, m - p). Only applies when method is DESeq2.
  • cooksFilter · boolean · optionnel
    set the p-value of genes with a Cook's-distance outlier to NA. Only applies when method is DESeq2.
  • filterByExpr · boolean · optionnel
    keep only genes edgeR's filterByExpr finds expressed (the edgeR and limma workflows' first step); off fits every gene. Only applies when method is edgeR-QL or limma-voom.
  • lfcThreshold · number · optionnel
    test |log2 fold change| against this threshold instead of 0. Only applies when method is DESeq2.
  • altHypothesis · string · optionnel · greaterAbs | greaterAbsUPSHOT | lessAbs | greater | less | greaterAbs2014
    which side of the threshold is the alternative. Only applies when method is DESeq2.
  • minTotalCount · number · optionnel
    filterByExpr: the total count a gene needs across all samples. Only applies when method is edgeR-QL or limma-voom.
  • pAdjustMethod · string · optionnel · holm | hochberg | hommel | bonferroni | BH | BY | fdr | none
    multiple-testing adjustment across genes (R `p.adjust`).
  • independentFiltering · boolean · optionnel
    drop low-mean genes from the adjustment when that gains rejections at `alpha`. Only applies when method is DESeq2.
  • minReplicatesForReplace · number · optionnel
    samples per group from which outlier counts are replaced and the gene refitted, instead of flagged. Only applies when method is DESeq2.

  Exemple d'appel

  {"name": "differential_expression", "arguments": {"counts": "texte", "samples": "texte"}}

  Exemple de retour

  {"content": [{"type": "text", "text": "…"}], "structuredContent": {"genes": "texte", "maPlot": {}, "summary": "texte", "upGenes": "texte", "volcano": {}, "downGenes": "texte", "rankedList": "texte", "testedGenes": "texte", "dispersionPlot": {}, "significantGenes": "texte"}}

• digest_fragments≈ 611 tokens

  Digest the subject with the given enzymes into real fragments (sequence + both overhangs). Emits the selected fragment as a NEW record, so a downstream gel/map/ORF runs on that fragment — the digest→assembly hand-off.

  Paramètres, retour & exemple (4)

  Paramètres

  • _files · array · optionnel
    The project: record references shaped like _subject. Their records become library documents a tool names in sequences/parts/document; a trace or alignment is found by file name.
  • enzymes · array · requis
    enzymes to digest with — resolved against the bundled cut catalog (REBASE spellings; smaller than the REBASE dossier the editor shows). Left unset, the run uses your active enzyme collection.
  • _subject · object · optionnel
    The record to act on: exactly one of sequence, accession (+source), sample (an id from list_samples) or file ({name, text} or {name, base64}); record_index picks one record of several.
  • fragment_index · number · optionnel
    which fragment to emit as the downstream record (0-based, in cut order).

  Exemple d'appel

  {"name": "digest_fragments", "arguments": {"enzymes": []}}

  Exemple de retour

  {"content": [{"type": "text", "text": "…"}], "structuredContent": {"count": 1, "record": {}, "lengths": "texte", "fragments": "texte", "parentSpan": "texte"}}

• digest_reaction_conditions≈ 760 tokens

  The reaction a digest needs, from NEB's own data: the NEBuffer that serves every enzyme together (scored on the WORST enzyme's percent activity, a star-activity buffer disqualified at any percent), the incubation temperature(s), any cofactor that must be added (SAM or ATP), and each product's heat-inactivation step, or the products NEB cannot heat-inactivate. One call is one tube: enzymes that need different temperatures or have no common buffer come back with `singleTube: false`. Needs no open record.

  Paramètres, retour & exemple (3)

  Paramètres

  • _files · array · optionnel
    The project: record references shaped like _subject. Their records become library documents a tool names in sequences/parts/document; a trace or alignment is found by file name.
  • enzymes · array · requis
    enzymes or NEB product names in one tube (EcoRI, BamHI-HF). A name NEB does not sell is returned under `unknown`, never dropped. Left unset, the run uses your active enzyme collection.
  • _subject · object · optionnel
    The record to act on: exactly one of sequence, accession (+source), sample (an id from list_samples) or file ({name, text} or {name, base64}); record_index picks one record of several.

  Exemple d'appel

  {"name": "digest_reaction_conditions", "arguments": {"enzymes": []}}

  Exemple de retour

  {"content": [{"type": "text", "text": "…"}], "structuredContent": {"buffer": "texte", "buffers": "texte", "unknown": "texte", "cofactors": "texte", "singleTube": true, "temperaturesC": "texte", "heatInactivation": "texte"}}

• discover_annotation_contradictions≈ 1168 tokens

  Find the signal peptides or transmembrane segments in reviewed human UniProt that a sequence predictor contradicts. Each feature backed by experiment (evidence code ECO:0000269) is scored to say what a confirmed feature looks like to the predictor; every other feature, annotated from similarity, sequence analysis or a rule, is ranked among those scores, and its conformal p-value (1 + experimental features scoring at or below it) / (experimental + 1) is corrected across all of them. Signal, by either predictor: von Heijne's weight-matrix score (EMBOSS sigcleave) of the cleavage site UniProt annotates, or DeepSig's probability that the protein carries a signal peptide at all (its eukaryotic network ensemble, from the first 96 residues). Transmembrane: the share of the segment the HMM-TM topology model labels membrane helix. A contradiction is a disagreement between two models, to be read, not a correction of UniProt: von Heijne's matrix and the HMM-TM model are weaker than the SignalP and TMHMM runs behind most such annotations; DeepSig is of their generation. The result carries a self-check, half the experimental features tested against the other half, whose calls are all false by construction.

  Paramètres, retour & exemple (7)

  Paramètres

  • alpha · number · optionnel
    false discovery rate at which an annotation is called contradicted.
  • _files · array · optionnel
    The project: record references shaped like _subject. Their records become library documents a tool names in sequences/parts/document; a trace or alignment is found by file name.
  • feature · string · optionnel · signal | transmembrane
    which annotation to test: signal peptides or transmembrane segments. Values: signal (Signal peptides), transmembrane (Transmembrane segments).
  • _subject · object · optionnel
    The record to act on: exactly one of sequence, accession (+source), sample (an id from list_samples) or file ({name, text} or {name, base64}); record_index picks one record of several.
  • decoding · string · optionnel · viterbi | posterior-viterbi | optimal-accuracy
    transmembrane only: which HMM-TM decoder labels the residues. N-best is left out: it takes minutes per long protein, and the corpus has 5,231. Values: viterbi (Viterbi), posterior-viterbi (Posterior-Viterbi), optimal-accuracy (Optimal accuracy). Only applies when feature is transmembrane. Advanced.
  • predictor · string · optionnel · von-heijne | deepsig
    signal only: von Heijne's matrix asks whether signal peptidase would cut where UniProt says; DeepSig asks whether the protein has a signal peptide at all (it loads 9.8 MB of network weights and runs twenty networks per protein, so it is far slower than the matrix). Values: von-heijne (von Heijne matrix), deepsig (DeepSig). Only applies when feature is signal.
  • correction · string · optionnel · BH | BY
    Benjamini–Hochberg (independent or positively dependent tests; conformal p-values against one calibration set are positively dependent) or Benjamini–Yekutieli (any dependence; less power). Values: BH (Benjamini–Hochberg), BY (Benjamini–Yekutieli).

  Exemple d'appel

  {"name": "discover_annotation_contradictions", "arguments": {"alpha": 1, "_files": [], "feature": "signal", "_subject": {}, "decoding": "viterbi", "predictor": "von-heijne"}}

  Exemple de retour

  {"content": [{"type": "text", "text": "…"}], "structuredContent": {"count": 1, "result": "texte", "selfCheck": "texte", "contradicted": "texte"}}

• discover_codon_outliers≈ 1433 tokens

  Score every coding sequence of a genome against the genome's own codon usage and report the genes whose synonymous codon choice that average does not explain, with the false discovery rate controlled across the genes. Records from different files are different genomes: each is scored against its own file's usage, and the false discovery rate is controlled once across every gene of every genome. Each gene gets Karlin's B and Supek & Vlahoviček's MILC against the pooled usage of the genes, and a G-test of its codon choice within each amino acid against that usage (χ², degrees of freedom from the amino acids it uses). Outliers are typically highly expressed genes (ribosomal proteins are the most deviant class), genes of unusual composition, and some of foreign origin; an outlier is NOT evidence of horizontal transfer, since codon bias is a poor indicator of transfer.

  Paramètres, retour & exemple (10)

  Paramètres

  • alpha · number · optionnel
    false discovery rate at which a gene is reported as an outlier.
  • _files · array · optionnel
    The project: record references shaped like _subject. Their records become library documents a tool names in sequences/parts/document; a trace or alignment is found by file name.
  • _subject · object · optionnel
    The record to act on: exactly one of sequence, accession (+source), sample (an id from list_samples) or file ({name, text} or {name, base64}); record_index picks one record of several.
  • alt_init · boolean · optionnel
    count every alternative start codon as Met throughout each gene, as coRdon does by default. Off reads an internal alternative start codon as its own amino acid. Advanced.
  • sequences · array · optionnel
    the genomes' coding sequences: wire upstream records here, or list library document names (each record of a CDS FASTA is one gene, read in frame from its first base; each file is one genome).
  • correction · string · optionnel · BH | BY
    Benjamini–Hochberg (independent or positively dependent tests) or Benjamini–Yekutieli (any dependence; less power). Values: BH (Benjamini–Hochberg), BY (Benjamini–Yekutieli).
  • file_codes · array · optionnel
    a genetic code for one file, as `file=code` (e.g. `Mycoplasma_genitalium_cds.fna=4`): that file's genes are read with it, every other file with genetic_code. For a corpus whose genomes translate differently. Advanced.
  • min_codons · number · optionnel
    genes with no more codons than this leave the reference and the result: the G-test's χ² limit is poor for short genes. In codons.
  • pool_files · boolean · optionnel
    score every named record as ONE genome, for a genome split across files (one per chromosome). Off: each file is its own genome, scored against its own usage.
  • genetic_code · number · optionnel · 1 | 2 | 3 | 4 | 5 | 6 | 9 | 10
    NCBI genetic code the genes are read with (4 for Mycoplasma, 11 for most bacteria; 1 and 11 group codons identically). Values: 1 (1 · Standard), 2 (2 · Vertebrate Mitochondrial), 3 (3 · Yeast Mitochondrial), 4 (4 · Mold Mitochondrial, Protozoan Mitochondrial, Coelenterate Mitochondrial, Mycoplasma, Spiroplasma), 5 (5 · Invertebrate Mitochondrial), 6 (6 · Ciliate Nuclear, Dasycladacean Nuclear, Hexamita Nuclear), 9 (9 · Echinoderm Mitochondrial, Flatworm Mitochondrial), 10 (10 · Euplotid Nuclear), 11 (11 · Bacterial, Archaeal and Plant Plastid), 12 (12 · Alternative Yeast Nuclear), 13 (13 · Ascidian Mitochondrial), 14 (14 · Alternative Flatworm Mitochondrial), 15 (15 · Blepharisma Macronuclear), 16 (16 · Chlorophycean Mitochondrial), 21 (21 · Trematode Mitochondrial), 22 (22 · Scenedesmus obliquus Mitochondrial), 23 (23 · Thraustochytrium Mitochondrial), 24 (24 · Rhabdopleuridae Mitochondrial), 25 (25 · Candidate Division SR1 and Gracilibacteria), 26 (26 · Pachysolen tannophilus Nuclear), 27 (27 · Karyorelict Nuclear), 28 (28 · Condylostoma Nuclear), 29 (29 · Mesodinium Nuclear), 30 (30 · Peritrich Nuclear), 31 (31 · Blastocrithidia Nuclear), 32 (32 · Balanophoraceae Plastid), 33 (33 · Cephalodiscidae Mitochondrial).

  Exemple d'appel

  {"name": "discover_codon_outliers", "arguments": {"alpha": 1, "_files": [], "_subject": {}, "alt_init": true, "sequences": [], "correction": "BH"}}

  Exemple de retour

  {"content": [{"type": "text", "text": "…"}], "structuredContent": {"genes": "texte", "result": "texte", "skipped": "texte", "outliers": "texte", "outlierCount": 1}}

• discover_flag_rates≈ 1176 tokens

  Measure how often a corpus of maps carries a cryptic σ70 promoter, a cryptic splice site or a synthesis-breaking repeat MORE EXTREME THAN CHANCE, rather than how many it carries. Every map of a few kilobases spells promoters, splice donors and repeats, so a raw hit count measures length and composition; here each map's own extreme (its most negative promoter ΔG, its highest MaxEntScan donor and acceptor score, its longest homopolymer, tandem repeat, repeated stretch and hairpin arm) is scored against k-let-preserving shuffles of that same map, and the false discovery rate is controlled across the corpus within each statistic. No statistic uses a threshold: none of the three models publishes one, and a vendor's repeat limit is a product's capability, which `check_manufacturability` answers instead. The result is a per-statistic rate with an exact binomial interval, plus every map's own test. Cost is dominated by the σ70 scan at roughly a third of a second per map per shuffle, so a corpus of maps at the default 99 shuffles is minutes of work; drop `flags` to the statistics you need to make it cheaper.

  Paramètres, retour & exemple (10)

  Paramètres

  • seed · number · optionnel
    seed for the shuffles. Each record draws from seed + its own index, so a record's answer does not depend on the rest of the corpus. Advanced.
  • alpha · number · optionnel
    false discovery rate at which a record counts towards a flag's rate.
  • flags · array · optionnel
    which statistics to run. Empty runs all seven.
  • _files · array · optionnel
    The project: record references shaped like _subject. Their records become library documents a tool names in sequences/parts/document; a trace or alignment is found by file name.
  • _subject · object · optionnel
    The record to act on: exactly one of sequence, accession (+source), sample (an id from list_samples) or file ({name, text} or {name, base64}); record_index picks one record of several.
  • shuffles · number · optionnel
    shuffles per record. The smallest p the null can give is 1 / (shuffles + 1), which is what bounds how small a corrected q can get.
  • sequences · array · optionnel
    the corpus: wire upstream records here, or list library document names. Each is one record of the sweep.
  • shuffle_k · number · optionnel
    k-let size the shuffles preserve. 2 holds every dinucleotide count, which is what all three statistics read.
  • correction · string · optionnel · BH | BY
    Benjamini–Hochberg (independent or positively dependent tests) or Benjamini–Yekutieli (any dependence; less power). Values: BH (Benjamini–Hochberg), BY (Benjamini–Yekutieli).
  • include_subject · boolean · optionnel
    also test the node's subject (the open or wired record).

  Exemple d'appel

  {"name": "discover_flag_rates", "arguments": {"seed": 1, "alpha": 1, "flags": [], "_files": [], "_subject": {}, "shuffles": 1}}

  Exemple de retour

  {"content": [{"type": "text", "text": "…"}], "structuredContent": {"hits": "texte", "rates": "texte", "sweep": "texte", "tests": "texte", "hitCount": 1, "nullModel": "texte"}}

• discover_gene_tree_discordance≈ 1243 tokens

  Find the genes whose own alignment rejects the species tree. Each named alignment file is one gene, its records the taxa, named as the species tree's tips. For every gene the species tree and each of its nearest-neighbour rearrangements (two per internal branch) is fitted by maximum likelihood under GTR + Γ (rates, base frequencies and shape fitted on the species tree, branch lengths refitted on each rearrangement), and the Shimodaira–Hasegawa test asks whether the species tree is significantly worse than the best of them; the false discovery rate is controlled across genes. A rejection says the gene fits another tree better: incomplete lineage sorting does that to a share of genes among closely spaced species, and so do hidden paralogy, alignment error and transfer, so it is a gene to read, never a call of any one of them. Also reports which genes' best tree is not the species tree, rejected or not, and which alternative trees they choose. Graded against phangorn's pml, optim.pml and SH.test on 122 great-ape genes. About a second of fitting per gene in a browser.

  Paramètres, retour & exemple (10)

  Paramètres

  • seed · number · optionnel
    seed for the bootstrap. Each gene draws from seed + its own index, so a gene's p does not depend on the rest of the corpus. Advanced.
  • alpha · number · optionnel
    false discovery rate at which a gene counts as rejecting the species tree.
  • _files · array · optionnel
    The project: record references shaped like _subject. Their records become library documents a tool names in sequences/parts/document; a trace or alignment is found by file name.
  • sh_form · string · optionnel · published | phangorn
    how each replicate is measured: from its best tree, as Shimodaira and Hasegawa (1999) and Goldman et al. (2000) define the test, or from its worst, as phangorn's SH.test computes it. They agree when the replicates are symmetric. Values: published (Published (from the best tree)), phangorn (phangorn (from the worst tree)). Advanced.
  • _subject · object · optionnel
    The record to act on: exactly one of sequence, accession (+source), sample (an id from list_samples) or file ({name, text} or {name, base64}); record_index picks one record of several.
  • alignments · array · requis
    the gene alignments: library file names, each an aligned multi-FASTA with one record per taxon, the record names being the species tree's tips.
  • correction · string · optionnel · BH | BY
    Benjamini–Hochberg (independent or positively dependent tests) or Benjamini–Yekutieli (any dependence; less power). Values: BH (Benjamini–Hochberg), BY (Benjamini–Yekutieli).
  • replicates · number · optionnel
    RELL bootstrap replicates of the SH test. The smallest nonzero p is 1 / replicates; a p of 0 means no replicate reached the observed difference, which evidence reads as 1 / (replicates + 1).
  • species_tree · string · requis
    the species tree in Newick, tips named as the alignments' records. Rooted or not; it is tested unrooted.
  • gamma_categories · number · optionnel
    discrete Gamma rate categories; 1 fits no rate variation among sites. Advanced.

  Exemple d'appel

  {"name": "discover_gene_tree_discordance", "arguments": {"alignments": [], "species_tree": "texte"}}

  Exemple de retour

  {"content": [{"type": "text", "text": "…"}], "structuredContent": {"genes": "texte", "sweep": "texte", "rejected": 1, "discordant": 1, "alternatives": "texte"}}

• discover_reference_concordance≈ 813 tokens

  Ask whether a reference-gene stability ranking holds across conditions, and which candidate genes rank well everywhere rather than in one tissue or treatment. Each condition (the Group column of a long-format Cq table) is ranked by geNorm on its own samples; the conditions are then the blocks of a Friedman test and Kendall's W says how far they agree (0 independent orders, 1 the same order everywhere), with an asymptotic χ² p and a Monte Carlo p from shuffling each condition's ranks. Returns every gene's rank in every condition, its mean rank (the meta-ranking) and its best and worst. geNorm cannot order its two most stable genes, so they share rank 1.5 in every condition. Use `rank_reference_genes` for one condition's ranking by all four algorithms.

  Paramètres, retour & exemple (5)

  Paramètres

  • seed · number · optionnel
    seed for the shuffles. Each permutation draws from its own stream, so one can be re-run alone. Advanced.
  • _files · array · optionnel
    The project: record references shaped like _subject. Their records become library documents a tool names in sequences/parts/document; a trace or alignment is found by file name.
  • _subject · object · optionnel
    The record to act on: exactly one of sequence, accession (+source), sample (an id from list_samples) or file ({name, text} or {name, base64}); record_index picks one record of several.
  • cq_table · string · requis
    the long-format table `Target,Sample,Group,Cq`, one row per measurement; Group is the condition each sample was measured in, and every gene must be measured in every sample.
  • permutations · number · optionnel
    shuffles of the ranks within each condition. The smallest p is 1 / (permutations + 1).

  Exemple d'appel

  {"name": "discover_reference_concordance", "arguments": {"cq_table": "texte"}}

  Exemple de retour

  {"content": [{"type": "text", "text": "…"}], "structuredContent": {"p": 1, "w": 1, "genes": "texte", "result": "texte", "nullModel": "texte", "conditions": "texte"}}