com.seqbench/workbench
Registry code: 0e1a57f2b9b128a1
SeqBench exposes 144 DNA, RNA and protein tools. Prefer these tools over ad-hoc sequence arithmetic. Most calls are deterministic read-only calculations, but random_sequence is intentionally random; external lookup, model and sidecar tools may change with their upstreams; session_create/session_set/session_run keep scratch values for 24 hours; and save_permalink writes a permanent anonymous result. For many records use batch; for a single-sequence pipeline use workflow. Every successful calculation includes gate and provenance metadata. A null gate means no objective gate exists, and every…
- endpoint
- https://seqbench.com/api/mcp
- protocol
- http-sse ·2025-06-18
- authentication
- none observed
- public key
- none — nobody has proven they own this listing
- karma
- 0 · newcomer
90 days 100%· all time 100%
last good check
of 144 tools
- unknown → live
The one measurement on this page that an operator cannot produce by editing a file on its own server: somebody else chose it, and paid to. Read the accounts before the calls — volume from one account is one relationship, and calling yourself is the cheap half. Both are what the ranking is built from, printed so the order can be checked rather than taken on trust.
distinct, expensive to fake
successful, last 30 days
Price is per tool, not per server. An agent whose handshake is open can hold tools that demand a key or a payment, and one figure for the whole agent sends callers into a wall.
format_sequence unknown never probed
Clean, case-fold, DNA↔RNA convert, reverse and line-wrap a sequence.
{ "type": "object", "required": [ "sequence" ], "properties": { "width": { "type": "integer", "default": 60, "description": "Line-wrap width; 0 = single line." }, "convert": { "enum": [ "none", "toRna", "toDna" ], "type": "string", "default": "none", "description": "DNA→RNA (T→U) or RNA→DNA (U→T)." }, "reverse": { "type": "boolean", "default": false, "description": "Reverse the sequence (no complement)." }, "caseMode": { "enum": [ "keep", "upper", "lower" ], "type": "string", "default": "keep" }, "sequence": { "type": "string", "residues": "nt", "description": "Nucleotide sequence (raw or FASTA; IUPAC accepted)." }, "stripNonLetters": { "type": "boolean", "default": true, "description": "Remove digits, spaces and gaps (keep letters only)." } }, "additionalProperties": false }arguments 48 linesmotif_finder unknown never probed
Find (overlapping) occurrences of an IUPAC motif on either strand, allowing mismatches.
{ "type": "object", "required": [ "sequence", "motif" ], "properties": { "limit": { "type": "integer", "default": 500, "maximum": 20000, "minimum": 1, "description": "How many matches to return. `count` always reports every hit found and `truncated` says whether the list was cut." }, "motif": { "type": "string", "residues": "nt", "description": "Query motif; IUPAC ambiguity codes (R Y S W K M B D H V N) allowed." }, "sequence": { "type": "string", "residues": "nt", "description": "Nucleotide sequence (raw or FASTA; IUPAC accepted)." }, "maxMismatches": { "type": "integer", "default": 0, "description": "Maximum allowed mismatches per match." }, "searchReverseStrand": { "type": "boolean", "default": true, "description": "Also search the reverse strand." } }, "additionalProperties": false }arguments 37 linesreverse_translate unknown never probed
Back-translate a protein to DNA (most-frequent codon per organism, or degenerate IUPAC consensus).
{ "type": "object", "required": [ "protein" ], "properties": { "mode": { "enum": [ "frequent", "degenerate" ], "type": "string", "default": "frequent" }, "protein": { "type": "string", "residues": "aa", "description": "Protein sequence (one-letter codes; * for stop)." }, "organism": { "enum": [ "ecoli", "human", "yeast", "cho", "pichia", "insect", "arabidopsis", "zebrafish" ], "type": "string", "default": "ecoli", "description": "Codon-usage host (ignored in degenerate mode)." } }, "additionalProperties": false }arguments 37 linesrandom_sequence unknown never probed
Generate a random DNA, RNA or protein sequence, optionally with a target GC content.
{ "type": "object", "required": [ "length" ], "properties": { "kind": { "enum": [ "dna", "rna", "protein" ], "type": "string", "default": "dna" }, "length": { "type": "integer", "default": 100, "description": "Number of residues to generate." }, "gcContent": { "type": "number", "description": "Target GC percentage 0..100 (dna/rna only); omit for uniform." } }, "additionalProperties": false }arguments 27 linesprotein_annotate_poll unknown never probed
Check an InterProScan job submitted via protein_annotate_submit. Returns {status, ready:false} while still running; once FINISHED, also returns the parsed domain architecture, per-match details and deduplicated GO terms.
{ "type": "object", "required": [ "jobId" ], "properties": { "jobId": { "type": "string" } }, "additionalProperties": false }arguments 12 linesplasmid_identify unknown never probed
Screen a query plasmid against a small curated set of common backbones (cloning vectors, expression vectors, BACs — see referencesChecked for the exact list) to identify which one(s) it resembles, separate an unmatched region (normal — your own insert) from a POSSIBLE CHIMERA (a region matching a different known backbone than its neighbor), and report per-match %identity/%coverage. NOT a search against Addgene's ~100k-plasmid catalog or PlasmidScope's 850k+ — a curated-set screen only.
{ "type": "object", "required": [ "sequence" ], "properties": { "topN": { "type": "integer", "default": 5, "description": "How many top-ranked backbone candidates to report." }, "circular": { "type": "boolean", "default": true, "description": "Treat the query as a circular molecule (most plasmids are)." }, "sequence": { "type": "string", "residues": "nt", "description": "Nucleotide sequence (raw or FASTA; IUPAC accepted)." } }, "additionalProperties": false }arguments 24 linesid_map_poll unknown never probed
Check a UniProt id-mapping job submitted via id_map_submit. Returns {status, ready:false} while still running; once FINISHED, also returns the mapped ids (normalized regardless of which target database was requested) and any ids that failed to map.
{ "type": "object", "required": [ "jobId" ], "properties": { "jobId": { "type": "string" } }, "additionalProperties": false }arguments 12 linesprime_editing_design unknown never probed
Design SpCas9 prime-editing pegRNAs for a substitution, insertion, deletion, or small replacement: for each usable NGG PAM it builds the spacer, a primer-binding-site (PBS) length sweep targeting a ~30 C melting temperature, the reverse-transcriptase template (RTT) that encodes the edit, and the full 3' extension, plus PE3 nicking-sgRNA suggestions 40-90 bp away on the opposite strand. Designs where the edit destroys the pegRNA's own PAM (preventing re-nicking of the edited allele) are ranked first. Coordinates: every pegRNA coordinate (protospacer span, nick position, editStart/editEnd) is 1-based inclusive in the submitted PRE-EDIT target's frame — the protospacer+PAM search runs on the unedited sequence, because Cas9 has to bind the allele you actually have. The one exception is edit-dependent PE3b nicking guides, which exist only once the edit is installed; each nickingGuides entry therefore carries a `coordinateFrame` field of "target" or "editedSequence" naming the frame its own start/end/nickToNickDistance are measured in, and for a length-changing edit the two frames differ downstream of the edit. Off-target activity is not evaluated (no in-browser reference genome).
{ "type": "object", "required": [ "target", "editStart", "editEnd" ], "properties": { "target": { "type": "string", "residues": "nt", "description": "Forward-strand target DNA (raw or FASTA), with flanking sequence around the intended edit." }, "editEnd": { "type": "integer", "description": "1-based inclusive end of the region being changed. For a pure insertion, set editEnd = editStart - 1." }, "editStart": { "type": "integer", "description": "1-based inclusive start of the region being changed." }, "pbsLength": { "type": "integer", "description": "Optional preferred PBS length to highlight; a full 8-17 nt sweep is always returned." }, "frameStart": { "type": "integer", "description": "Optional 1-based CDS reading-frame start, used only to annotate whether a PAM-blocking mutation would be silent." }, "insertedSeq": { "type": "string", "default": "", "residues": "nt", "description": "Replacement bases (forward strand). Empty string means a deletion." }, "rttHomology": { "type": "integer", "default": 13, "description": "Homology length (nt) 3' of the edit that the RTT should include (typically 10-16)." } }, "additionalProperties": false }arguments 43 linessession_set unknown never probed
Add or overwrite named entries in an existing session.
{ "type": "object", "required": [ "sessionId", "entries" ], "properties": { "entries": { "type": "object", "description": "Named entries to add/overwrite, e.g. {\"insert\": \"...\"}.", "additionalProperties": { "type": "string" } }, "sessionId": { "type": "string" } }, "additionalProperties": false }arguments 20 linesreverse_complement unknown never probed
Reverse, complement and reverse complement of a DNA or RNA sequence.
{ "type": "object", "required": [ "sequence" ], "properties": { "type": { "enum": [ "dna", "rna" ], "type": "string", "default": "dna" }, "sequence": { "type": "string", "residues": "nt", "description": "Nucleotide sequence (raw or FASTA; IUPAC accepted)." } }, "additionalProperties": false }arguments 22 linesgc_content unknown never probed
GC content, AT content and per-base composition of a sequence.
{ "type": "object", "required": [ "sequence" ], "properties": { "sequence": { "type": "string", "residues": "nt", "description": "Nucleotide sequence (raw or FASTA; IUPAC accepted)." } }, "additionalProperties": false }arguments 14 linestranslate unknown never probed
Translate a nucleotide sequence to protein (single frame or all six frames; standard code).
{ "type": "object", "required": [ "sequence" ], "properties": { "frame": { "enum": [ 1, 2, 3 ], "type": "integer", "default": 1 }, "toStop": { "type": "boolean", "default": false, "description": "Stop at the first stop codon." }, "sequence": { "type": "string", "residues": "nt", "description": "Nucleotide sequence (raw or FASTA; IUPAC accepted)." } }, "additionalProperties": false }arguments 28 linesfind_orfs unknown never probed
Find open reading frames (ATG…stop) across all six frames.
{ "type": "object", "required": [ "sequence" ], "properties": { "limit": { "type": "integer", "default": 100, "maximum": 5000, "minimum": 1, "description": "How many ORFs to return, longest first. `count` always reports every ORF found and `truncated` says whether the list was cut." }, "sequence": { "type": "string", "residues": "nt", "description": "Nucleotide sequence (raw or FASTA; IUPAC accepted)." }, "minAaLength": { "type": "integer", "default": 30, "description": "Minimum protein length (aa) to report." }, "requireStop": { "type": "boolean", "default": false, "description": "Only report ORFs terminated by a stop codon." } }, "additionalProperties": false }arguments 31 linesdouble_digest unknown never probed
Recommend a single NEB buffer (and flag caveats) for digesting with two enzymes in one tube.
{ "type": "object", "required": [ "enzymeA", "enzymeB" ], "properties": { "enzymeA": { "type": "string", "description": "First enzyme name (e.g. EcoRI)." }, "enzymeB": { "type": "string", "description": "Second enzyme name (e.g. BamHI)." } }, "additionalProperties": false }arguments 18 linesgel_band_size unknown never probed
Calibrate a gel lane against a marked DNA ladder and read the size of any other band from how far it ran. Migration distance is approximately linear in log(size) over a gel's resolving range, so a least-squares line through the marked rungs interpolates between them — and NOT outside them, which is why a band beyond the marked span comes back flagged `extrapolated` rather than quietly clamped to the nearest rung. Reports R² and the per-rung residual, because one mis-marked rung (a doublet marked as one band, a mis-clicked centre) shifts every size on the gel and a single R² hides it. Distances may be in pixels, millimetres or anything else, as long as they are all measured the same way from the same reference line.
{ "type": "object", "required": [ "ladder", "ladderDistances" ], "properties": { "ladder": { "type": "string", "description": "Which ladder is in the marked lane. One of: 1 kb, 1 kb Plus, 100 bp." }, "bandDistances": { "type": "array", "items": { "type": "number" }, "description": "How far each band you want a size for ran, in the same unit from the same reference line. May be empty: the fit and its per-rung residuals are an answer on their own, and are how you find out the ladder was marked correctly before reading anything off it." }, "ladderDistances": { "type": "array", "items": { "type": "number" }, "description": "How far each visible ladder band ran, in any consistent unit, measured from the same reference line (the well) as the query bands. Order does not matter — they are sorted and matched to the ladder's sizes largest-first, since a larger fragment runs less far. At least 3: two points fit a line exactly, so they cannot show whether the ladder was marked correctly." } }, "additionalProperties": false }arguments 28 linessanger_plate_verify unknown never probed
Judge a whole plate of Sanger reads against one construct and return one row per clone: PASS, POINT_MUTATION, INDEL, VECTOR_ONLY (the insert is absent), WRONG_INSERT (the backbone matches and the insert does not), LOW_COVERAGE, or AMBIGUOUS. Reads are grouped into clones from their FASTA/FASTQ record names (facility conventions like PlateA_A01_pXY-1_M13F, pXY-1_T7-F, 2026-08-01_pXY_clone3_R), and every read's assignment is reported with a confidence so a grouping can be corrected rather than trusted. Each clone's reads are piled up in reference coordinates, so a difference one read reports where other covering reads read the reference is reported as the sequencing error it is, not as a mutation — and a position no read covered is never PASS. Every verdict cites the positions it rests on. Give insertStart/insertEnd to have clones judged over the insert alone, which is also what VECTOR_ONLY and WRONG_INSERT need.
{ "type": "object", "required": [ "reference", "reads" ], "properties": { "reads": { "type": "string", "maxLength": 2000000, "description": "All the plate's reads as FASTA or FASTQ (auto-detected). The record name is what the clone grouping is read from. Up to 384 reads / 400,000 total bases, and (reference length x total read bases) must stay under 200,000,000 — split a 96-clone plate across calls." }, "circular": { "type": "boolean", "default": false, "description": "Treat the construct as a plasmid, so a read crossing its arbitrary linear start is aligned through the join instead of having its tail discarded." }, "grouping": { "enum": [ "auto", "one-clone", "per-read" ], "type": "string", "default": "auto", "description": "How reads become clones. \"auto\" parses the record names; \"one-clone\" treats every read as being of one clone (use when the names carry nothing); \"per-read\" judges each read on its own." }, "insertEnd": { "type": "integer", "minimum": 1, "description": "1-based last base of that stretch." }, "reference": { "type": "string", "residues": "nt", "description": "The intended construct (raw or FASTA). Up to 20,000 bp." }, "insertLabel": { "type": "string", "description": "What to call it in the verdicts. Default \"the insert\"." }, "insertStart": { "type": "integer", "minimum": 1, "description": "1-based first base of the stretch that has to be right (the insert). With insertEnd, every clone is judged over this span alone — the only honest framing when one 900 bp read cannot cover a 6 kb plasmid — and VECTOR_ONLY/WRONG_INSERT become reachable. May be greater than insertEnd on a circular construct, meaning the span crosses the origin." }, "qualityOffset": { "enum": [ 33, 64 ], "type": "integer", "default": 33, "description": "ASCII offset of the FASTQ quality string. 33 for anything modern, 64 for pre-1.8 Illumina." }, "trimThreshold": { "type": "integer", "default": 20, "maximum": 60, "minimum": 0, "description": "Phred threshold for trimming both ends of a read (BWA's rule). Only applies to FASTQ input, which is the only input that carries quality." } }, "additionalProperties": false }arguments 65 linescrispr_grna_design unknown never probed
Find and score candidate guide RNAs (protospacer + PAM) in a target DNA for common nucleases (SpCas9, SpCas9-NG, SaCas9, Cas12a). PREDICTED, NOT MEASURED. No held-out skill statistic is claimed. Both are pre-2016 models, superseded by Rule Set 3 (DeWeirdt et al., Nat Commun 2022) and by DeepHF. Rule Set 3 IS now shipped here, as crispr_ontarget, and unlike these two it carries a held-out calibration: on an independent tiling library, 87.7% / 74.9% / 82.0% of its lowest-scoring guides landed in the bottom two activity quintiles. Prefer it for SpCas9 with an NGG PAM; DeepHF is still not shipped. Treat these two as a ranking aid, not an efficiency prediction. Valid for: SpCas9 with an NGG PAM and a 20 nt spacer, and only when enough genomic flanking context is present to build the model's 30-mer / 35-mer window — both scores are null rather than padded otherwise. Nothing is predicted for SaCas9, Cas12a or SpCas9-NG.
{ "type": "object", "required": [ "sequence" ], "properties": { "minScore": { "type": "number", "default": 0, "description": "Only return guides with a heuristic score at least this high (0–100)." }, "nuclease": { "enum": [ "spcas9", "spcas9ng", "sacas9", "cas12a" ], "type": "string", "default": "spcas9", "description": "Nuclease id. Omit to just list the available nucleases (no scan is performed)." }, "sequence": { "type": "string", "residues": "nt", "description": "Nucleotide sequence (raw or FASTA; IUPAC accepted)." }, "searchReverseStrand": { "type": "boolean", "default": true, "description": "Also scan the reverse strand for guides." } }, "additionalProperties": false }arguments 35 linesplasmid_deep_annotate unknown never probed
Annotate a plasmid against pLannotate's open-source feature library — a much larger signature set (GenoLIB parts + Swiss-Prot + FPbase + Rfam, cross-referenced against ~195k Addgene-deposited plasmids) than plasmid_annotate's built-in curated list, and it reports partial and low-identity hits as graded alignments rather than the pass/fail signature match plasmid_annotate does (that one is not exact-only either — signatures of 20 bp or more tolerate up to ~10% mismatches — but it reports a hit or nothing, with a `mismatches` count and an `exact` flag). Each feature here carries its percent identity, reference coverage and a fragment flag so you can judge a weak hit. Runs a multi-second search on a shared service and is therefore rate limited (see 429/503); use plasmid_annotate for an instant, unmetered first pass.
{ "type": "object", "required": [ "sequence" ], "properties": { "circular": { "type": "boolean", "default": true, "description": "Treat the sequence as a circular plasmid (vs. linear)." }, "sequence": { "type": "string", "description": "Nucleotide sequence (raw or FASTA). A, C, G, T, N only — other IUPAC codes are rejected rather than silently dropped, because pLannotate's search engines discard them and every coordinate after would shift. Max 150,000 bp." } }, "additionalProperties": false }arguments 18 linesverify_construct unknown never probed
Re-derive a construct's insert from the PCR (template + primers) claimed to have produced it, then check — independently of that claim — whether the expected insert actually appears (either orientation) in the claimed final construct, at what identity, and with exact mismatch positions if not. Optionally also checks for a premature stop in a declared reading frame. Primers may carry a non-templated 5' tail (a restriction site, a Gibson arm, a tag): a construct missing ONLY tail bases still passes, since that is exactly what digesting a tailed amplicon removes before ligation — see match.templateCoveragePct and match.unalignedIsTailOnly, and note the pass does not establish that the right enzyme made the cut. This re-derives from the claim's own stated inputs; it does not review the claim's prose.
{ "type": "object", "required": [ "claimedConstruct", "insertTemplate", "insertForwardPrimer", "insertReversePrimer" ], "properties": { "insertTemplate": { "type": "string", "residues": "nt", "description": "PCR template the insert was amplified from." }, "claimedConstruct": { "type": "string", "residues": "nt", "description": "The final sequence claimed to have been built." }, "templateCircular": { "type": "boolean", "default": false, "description": "Treat insertTemplate as circular (e.g. amplifying from a plasmid)." }, "constructCircular": { "type": "boolean", "default": false, "description": "Treat claimedConstruct as a circular plasmid, so an insert that spans its arbitrary numbering origin is found whole. Without it the insert is looked for linearly and a wrapped one covers only its longer half." }, "expectedFrameStart": { "type": "integer", "description": "1-based position in claimedConstruct where the intended reading frame begins. If given, flags a premature stop before the end of the aligned insert region." }, "insertForwardPrimer": { "type": "string", "residues": "nt", "description": "Forward primer used to amplify the insert, 5'→3'." }, "insertReversePrimer": { "type": "string", "residues": "nt", "description": "Reverse primer used to amplify the insert, 5'→3'." }, "maxPrimerMismatches": { "type": "integer", "default": 0, "maximum": 10, "minimum": 0, "description": "Mismatches tolerated per primer during PCR prediction (0–10)." } }, "additionalProperties": false }arguments 53 linesaso_design unknown never probed
Design antisense-oligonucleotide (ASO) gapmers against an mRNA target: scans candidate sites, builds the antisense oligo in the standard 5-10-5 architecture (chemically-modified wings, central DNA gap for RNase H1, phosphorothioate backbone), and screens each for known liabilities (G-quadruplex motifs, CpG immunostimulation, self-complementarity, GC extremes). No transcriptome-wide off-target search.
{ "type": "object", "required": [ "target" ], "properties": { "wing": { "type": "integer", "default": 5, "minimum": 0, "description": "Modified-wing length on each side (nt); the central gap = length − 2×wing, so 2×wing must be less than length." }, "length": { "type": "integer", "default": 20, "maximum": 50, "minimum": 8, "description": "Total gapmer length (nt). A real RNase H1 gapmer is 12-25." }, "target": { "type": "string", "residues": "nt", "description": "Nucleotide sequence (raw or FASTA; IUPAC accepted)." } }, "additionalProperties": false }arguments 27 linesgolden_gate_fidelity unknown never probed
Score a candidate set of 4-base Golden Gate/MoClo junction overhangs against real published T4-ligase ligation-count data: per-overhang specificity, the weakest link in the set, and any risky cross-reacting pairs. Optionally compare against a named published overhang set. This is SeqBench's own transparent scoring methodology — it does not reproduce NEB's/Potapov's own published aggregate fidelity percentages for named sets (their exact formula isn't disclosed anywhere accessible).
{ "type": "object", "required": [ "overhangs" ], "properties": { "dataset": { "enum": [ "generic-t4-37c-1h", "bsai-hfv2" ], "type": "string", "default": "generic-t4-37c-1h", "description": "Which real ligation dataset to score against — generic T4 ligase, or an enzyme-specific one-pot dataset if that matches your actual digestion enzyme." }, "overhangs": { "type": "array", "items": { "type": "string" }, "description": "The candidate 4-base overhangs for one assembly (e.g. [\"GGAG\",\"TACT\",\"AATG\"]). At least 2, no duplicates." }, "riskThreshold": { "type": "number", "default": 0.05, "description": "Flag a pair as risky when the cross-reaction is at least this fraction of that pair's own total signal." }, "compareToNamedSet": { "enum": [ "pryor-2020-plant-11", "pryor-2020-20set", "cidar-moclo" ], "type": "string", "description": "Also score this published reference set (see namedSetsAvailable in the output) alongside your candidate set, for comparison." } }, "additionalProperties": false }arguments 39 linesgolden_gate_design unknown never probed
CHOOSE a set of 4-base Golden Gate/MoClo junction overhangs, rather than scoring one you already have. Maximizes the fidelity of the set's WEAKEST junction against the same published T4-ligase ligation data golden_gate_fidelity scores with, subject to every member actually ligating well — an overhang can score a perfect ratio simply because nothing was ever measured cross-reacting with it, and 94% of the ligation matrix is zeros. Pin the overhangs your vector already commits you to with `fixed`, forbid others with `forbidden`, and give `junctions` when the junctions sit at real positions in real sequence and may only slide a few bases. Reports whether the search was exhaustive (provably the best available) or budget-limited (the best found).
{ "type": "object", "required": [ "count" ], "properties": { "count": { "type": "integer", "maximum": 40, "minimum": 2, "description": "How many junctions the assembly has, INCLUDING any given in `fixed`." }, "fixed": { "type": "array", "items": { "type": "string" }, "description": "Overhangs that must appear — typically the ones the destination vector already commits you to. Scored like any other member; simply not swappable." }, "dataset": { "enum": [ "generic-t4-37c-1h", "bsai-hfv2" ], "type": "string", "default": "generic-t4-37c-1h", "description": "Which real ligation dataset to optimize against." }, "forbidden": { "type": "array", "items": { "type": "string" }, "description": "Overhangs the design may not use, whatever they score." }, "junctions": { "type": "array", "items": { "type": "object" }, "description": "One entry per junction still to be chosen, as {sequence, position, slide}: the construct sequence, the 1-based first base of the preferred overhang, and how many bases either side the junction may move. Use this instead of a free design when the junctions are real places in real DNA — the candidates then come from bases that actually exist. Length must equal count minus fixed." }, "minCorrectSignal": { "type": "number", "description": "Reject any overhang whose own correct-join signal is below this. Defaults to the chosen dataset's MEDIAN diagonal (2,694 for generic T4, 520 for BsaI-HFv2 — they differ five-fold, which is why this is derived rather than fixed). Set 0 to allow every overhang." } }, "additionalProperties": false }arguments 49 linessave_permalink unknown never probed
Run a registered tool and save its (arguments, result) pair under a short permanent code that anyone with the link can view read-only (/permalink/{code}). Use this to cite or share a specific result (e.g. a verify_construct or verify_assembly check) rather than re-pasting it.
{ "type": "object", "required": [ "tool", "args" ], "properties": { "args": { "type": "object", "description": "Arguments for that tool, exactly as you would pass to it directly." }, "tool": { "type": "string", "description": "Name of the registered tool to run and save (e.g. \"verify_construct\")." } }, "additionalProperties": false }arguments 18 linesoutcome_deconvolve unknown never probed
Decompose one Sanger trace into fractions over a set of candidate molecules — the intended construct, the empty backbone, a double insert, a flipped part — instead of onto a generic indel ladder. Non-negative least squares against the candidates' own sequences, so no molecule is ever assigned a negative share. Reports the R² of the fit, which is what says whether the tube holds anything outside the candidate set, and GROUPS candidates the read cannot tell apart rather than splitting their share between them. Feed it the alternatives from assembly_outcomes. PREDICTED, NOT MEASURED. Every run reports its own R²: how much of the observed per-position composition the candidate basis explains. That is a measured adequacy on YOUR trace, and a low value is a statement that the tube holds something the candidate set does not contain. No accuracy against a reference method is published for this implementation, and none is quoted. Exact recovery of synthetic mixtures is deliberately NOT offered as validation: it tests the arithmetic, not whether a real capillary trace behaves like the model. Valid for: One read, from one primer, over a set of candidate molecules that all contain that primer's site and differ from each other within the read. Fractions are reported per GROUP of candidates the read cannot tell apart, and that grouping is part of the answer. NOT valid when the read's anchor identity to a candidate is low (it does not share the primer region), nor when R² comes back low, nor for telling apart candidates that differ only outside the read.
{ "type": "object", "required": [ "readBases", "readChannels", "candidates" ], "properties": { "readBases": { "type": "string", "residues": "nt", "description": "Base calls of the read, e.g. from parse_sanger_trace." }, "candidates": { "type": "array", "items": { "type": "object" }, "description": "The molecules this reaction could have produced, as { id, label, sequence, circular? }. Between 2 and 24; assembly_outcomes' intended plus alternatives is the intended source." }, "readChannels": { "type": "array", "items": { "type": "array", "items": { "type": "number" } }, "description": "Per-base [A, C, G, T] intensities, one row per called base, read at that base's peak location." } }, "additionalProperties": false }arguments 33 linesprotein_hydrophobicity unknown never probed
Sliding-window hydropathy/hydrophobicity profile (ProtScale-style) over a published amino-acid scale.
{ "type": "object", "required": [ "sequence" ], "properties": { "scale": { "enum": [ "Kyte-Doolittle", "Hopp-Woods", "Eisenberg" ], "type": "string", "default": "Kyte-Doolittle", "description": "Amino-acid scale. Kyte-Doolittle and Eisenberg are hydrophobicity; Hopp-Woods is hydrophilicity." }, "window": { "type": "integer", "default": 9, "description": "Sliding-window size (clamped to an odd number ≥ 1)." }, "sequence": { "type": "string", "residues": "aa", "description": "Protein sequence (one-letter amino-acid codes; non-AA characters ignored)." } }, "additionalProperties": false }arguments 29 linesseqfile_stats unknown never probed
Statistics for a FASTA or FASTQ file: count, length distribution, N50, GC content and (FASTQ) mean quality.
{ "type": "object", "required": [ "input" ], "properties": { "input": { "type": "string", "description": "FASTA or FASTQ text (raw sequence is treated as single-record FASTA)." }, "qualityOffset": { "enum": [ 33, 64 ], "type": "integer", "default": 33, "description": "ASCII offset of the FASTQ quality string. 33 for anything modern, 64 for pre-1.8 Illumina." } }, "additionalProperties": false }arguments 22 linessession_get unknown never probed
Fetch named entries from a session. Prefer session_run for actually USING the values — it keeps raw sequences out of your context. Use this mainly to inspect or debug what a session currently holds.
{ "type": "object", "required": [ "sessionId" ], "properties": { "names": { "type": "array", "items": { "type": "string" }, "description": "Only return these entries; omit to return all of them." }, "sessionId": { "type": "string" } }, "additionalProperties": false }arguments 19 linesbarcode_design unknown never probed
Build a set of DNA barcodes that are pairwise at least a chosen edit distance apart, so a read error cannot turn one barcode in the pool into another. Honours a GC window, a homopolymer cap and excluded motifs (the restriction sites you clone with) during the search rather than filtering afterwards, and can extend a set you already have rather than replacing it. Reports the distance ACHIEVED — re-derived over the finished pool, not assumed from the search — plus how many read errors that distance lets you correct and detect. Deterministic given a seed. Returns fewer barcodes than asked, with a reason, when the constraints leave no room.
{ "type": "object", "required": [], "properties": { "seed": { "type": "integer", "default": 1, "description": "Seeds the search. Change it for a different set from the same constraints; keep it to reproduce one." }, "count": { "type": "integer", "default": 96, "maximum": 1000, "minimum": 1, "description": "How many barcodes to design (max 1000). A plate is 96 or 384." }, "gcMax": { "type": "number", "default": 75, "maximum": 100, "minimum": 0, "description": "Highest GC% a barcode may have." }, "gcMin": { "type": "number", "default": 25, "maximum": 100, "minimum": 0, "description": "Lowest GC% a barcode may have." }, "length": { "type": "integer", "default": 12, "maximum": 40, "minimum": 4, "description": "Barcode length in bases (default 12). Longer barcodes make a given distance far easier to reach." }, "metric": { "enum": [ "levenshtein", "hamming" ], "type": "string", "default": "levenshtein", "description": "'levenshtein' counts substitutions, insertions and deletions — the right choice for nanopore or PacBio, and the safe default. 'hamming' counts substitutions only, which is faster and adequate when the platform's errors are substitutions (Illumina), but gives NO protection against an indel shifting one barcode into another." }, "exclude": { "type": "array", "items": { "type": "string" }, "description": "Motifs no barcode may contain, checked on both strands — the restriction sites you clone with. Literal ACGT only." }, "existing": { "type": "array", "items": { "type": "string" }, "description": "Barcodes you already use. They are held fixed and the new ones are kept distant from them, so a second plate does not collide with the first." }, "minDistance": { "type": "integer", "default": 3, "minimum": 1, "description": "Minimum edit distance between any two barcodes (default 3). Distance 3 corrects one read error and detects two; distance 5 corrects two. Distance 1 only means 'not identical' and corrects nothing." }, "maxHomopolymer": { "type": "integer", "default": 3, "minimum": 1, "description": "Longest run of one base allowed (default 3). Homopolymers miscall on every platform and are the one composition rule worth keeping tight." } }, "additionalProperties": false }arguments 75 linesverify_assembly unknown never probed
Deterministic self-check: given the same method/parts cloning_simulate would use (restriction-ligation, Gibson, Golden Gate, LIC, SLIC or In-Fusion/CPEC — optionally deriving a part by in-silico PCR first), re-derive the expected WHOLE product and diff it against a claimed final sequence. Returns pass/fail plus the exact position and nature of any discrepancy — not an opinion, the same deterministic simulation SeqBench already runs, run a second time as a check. A recipe that can give more than one molecule is checked against ALL of them and `matchedCandidate` names the one the claim matched: a non-directional ligation really does put the insert in both ways round (half the plate carries each), a vector cut more than twice offers more than one backbone, and a Gibson junction whose fragments already share terminal sequence has two honest readings (one homology arm, or a tandem repeat present twice). See verify_construct for a narrower, insert-only check that doesn't require declaring the vector/enzymes/method.
{ "type": "object", "required": [ "method", "claimedConstruct" ], "properties": { "names": { "type": "array", "items": { "type": "string" }, "description": "Optional labels for each fragment." }, "coding": { "type": "boolean", "default": false, "description": "Report amino-acid effects of any mismatch, assuming claimedConstruct is (or contains) a coding sequence." }, "enzyme": { "type": "string", "default": "BsaI", "description": "Type IIS enzyme for Golden Gate — one of BsaI, BbsI, Esp3I (BsmBI); \"BsmBI\" also resolves to Esp3I, and NEB's variant names (BsaI-HFv2, BbsI-HF, BsmBI-v2) fold to the parent enzyme. Any other name fails the verification outright rather than being substituted." }, "insert": { "type": "string", "residues": "nt", "description": "Insert sequence (restriction and lic methods). Omit if insertPcr is given." }, "method": { "enum": [ "restriction", "gibson", "goldengate", "lic", "slic", "infusion" ], "type": "string", "description": "Assembly method used. restriction/gibson/goldengate are the primer-and-enzyme methods; lic and slic re-run the T4-polymerase chew-back (sequence-defined and time-stopped respectively) and infusion is In-Fusion/CPEC. Anything else is refused rather than substituted — see the note on \"topo\"." }, "vector": { "type": "string", "residues": "nt", "description": "Vector sequence (restriction and lic methods; for lic, the LINEARIZED vector). Omit if vectorPcr is given." }, "enzyme3": { "type": "string", "default": "BamHI", "description": "Insert 3′ enzyme (restriction method)." }, "enzyme5": { "type": "string", "default": "EcoRI", "description": "Insert 5′ enzyme (restriction method)." }, "circular": { "type": "boolean", "default": true, "description": "Treat the product/claimed construct as circular (most plasmids are)." }, "fragments": { "type": "array", "items": { "type": "string" }, "maxItems": 24, "description": "Fragments (5′→3′), assembled head-to-tail (gibson/goldengate/slic/infusion). BARE parts only — for gibson do NOT include the homology arms, which are added by the assembly primers and merged (so the product is fragment1+…+fragmentN). The convention is the OPPOSITE for slic and infusion: there the homology must already BE on the fragments (it arrived on the PCR primer tails), and infusion derives the ORDER from those homologies, so the order listed here is ignored. Use \"\" as a placeholder for any fragment supplied instead via the matching fragmentPcrs[i]." }, "insertPcr": { "type": "object", "description": "Derive the insert by PCR instead: {template, forwardPrimer, reversePrimer, maxMismatches? (0-10), circular?}." }, "vectorPcr": { "type": "object", "description": "Derive the vector by PCR instead: {template, forwardPrimer, reversePrimer, maxMismatches? (0-10), circular?}." }, "frameStart": { "type": "integer", "default": 1, "description": "1-based reading-frame start on claimedConstruct, used when coding is true." }, "overlapLen": { "type": "integer", "default": 20, "description": "Gibson homology-arm length (bp) that the assembly PRIMERS add at each junction. Since the fragments themselves must not carry their arms, this describes the junction/primer design only — it does not change the predicted product length or the verdict." }, "armTmTarget": { "type": "number", "default": 60, "description": "Target annealing Tm (°C) for primer arms." }, "chewBackLen": { "type": "integer", "default": 0, "minimum": 0, "description": "slic method: nucleotides removed from each 3′ end. A SLIC chew-back has no dNTP to arrest it and is stopped by time, so this is an input rather than a property of the sequence. 0 (default) models the intended reaction — chewed to the full homology and no further." }, "homologyLen": { "type": "integer", "default": 15, "minimum": 15, "description": "infusion method: terminal homology required at every junction, in bp. At least 15 — the junction is annealed and extended by a polymerase with no exonuclease to widen it and no ligase to seal it, so a shorter overlap is a different chemistry rather than a weaker version of this one." }, "fragmentPcrs": { "type": "array", "items": { "type": "object" }, "description": "Parallel to fragments, same length: null (or omit) to use fragments[i] directly, or a PCR spec {template, forwardPrimer, reversePrimer, maxMismatches? (0-10), circular?} to derive that fragment instead." }, "vectorEnzyme3": { "type": "string", "description": "Vector 3′ enzyme (restriction method); defaults to enzyme3." }, "vectorEnzyme5": { "type": "string", "description": "Vector 5′ enzyme (restriction method); defaults to enzyme5. Set a different, compatible enzyme (e.g. BglII for a BamHI insert) to verify heterologous-overhang cloning." }, "claimedConstruct": { "type": "string", "residues": "nt", "description": "The sequence you claim you ended up with." }, "insertNucleotide": { "enum": [ "A", "C", "G", "T" ], "type": "string", "description": "lic method: the single dNTP the INSERT's chew-back was run with. Normally the COMPLEMENT of vectorNucleotide (the classic pair is dTTP on the vector, dATP on the insert)." }, "vectorNucleotide": { "enum": [ "A", "C", "G", "T" ], "type": "string", "description": "lic method: the single dNTP the VECTOR's chew-back was run with (T for dTTP…). Required — T4 pol's exonuclease stops at the first occurrence of this base reading inward from each 3′ end, so there is no product to check against without it." }, "mergePreAddedArms": { "type": "boolean", "default": true, "description": "Gibson only. When two fragments already share terminal sequence, count that share ONCE (the default — the fragments already carry their arm) or set false to concatenate it twice, which is the right reading when the shared block is a genuine tandem repeat. You should rarely need this: the check tries BOTH readings and reports which one matched in `matchedCandidate`. Setting it restricts the check to one." }, "dephosphorylateVector": { "type": "boolean", "default": false, "description": "The linearized vector was CIP/rSAP-dephosphorylated (restriction method). Affects the self-ligation background warnings, not the product." } }, "additionalProperties": false }arguments 157 linesmelting_temperature unknown never probed
Primer/oligo melting temperature: nearest-neighbor (SantaLucia 1998) at the supplied reaction conditions, recommended from 14 nt up, with the Wallace rule for shorter oligos, a fixed-100 mM-Na+ Schildkraut-Lifson reference estimate, and molecular weights.
{ "type": "object", "required": [ "sequence" ], "properties": { "mgMM": { "type": "number", "default": 1.5, "description": "Divalent cation [Mg2+] (mM)." }, "naMM": { "type": "number", "default": 50, "description": "Monovalent cation [Na+]/[K+] (mM)." }, "dntpMM": { "type": "number", "default": 0.2, "description": "Total [dNTP] (mM), chelates Mg2+." }, "oligoNM": { "type": "number", "default": 250, "description": "Total strand concentration (nM)." }, "sequence": { "type": "string", "residues": "nt", "description": "Nucleotide sequence (raw or FASTA; IUPAC accepted)." }, "targetTm": { "type": "number", "description": "Optional target Tm (°C). When given, the response includes a pass/fail gate." }, "tmTolerance": { "type": "number", "default": 2, "description": "Allowed +/- window (°C) around targetTm for the gate." } }, "additionalProperties": false }arguments 43 linesannealing_temperature unknown never probed
Annealing temperature and a full cycling program for a primer PAIR, under the rule the polymerase's own vendor publishes — which is not one rule, and is only defined against the vendor's own Tm. For NEB products the Tm is computed exactly as NEB's Tm calculator computes it (SantaLucia 1998 nearest-neighbor with NEB's salt correction, at that product's own buffer and primer concentration — the same primer's Tm moves ~10 °C between NEB buffers) and NEB's calculator rule is applied to it: Q5 at Tm + 1, Phusion at 0.93 × Tm + 7.5 (both ABOVE the Tm), Taq/OneTaq/LongAmp at Tm − 5, Vent/Deep Vent at Tm − 2 above 20 nt, with NEB's ceilings. Toyobo KOD One is Tm − 5 at the salt and oligo concentration its manual names, Takara PrimeSTAR Max a FIXED 55 °C the primer Tm plays no part in (its own 2(A+T)+4(G+C)−5 sets only the annealing time), and a generic Taq/Pfu row applies the Tm − 3 to − 5 rule of thumb to a default-condition nearest-neighbor Tm. Returns denaturation/annealing/extension steps, cycle count, magnesium guidance, the Tm basis and vendor document behind each figure, and the same primers under every other polymerase in the table for comparison.
{ "type": "object", "required": [ "forwardPrimer", "reversePrimer", "polymerase" ], "properties": { "ampliconBp": { "type": "integer", "description": "Expected product length (bp), used for the extension time. Omit to get the per-kb rate without a time." }, "polymerase": { "type": "string", "description": "Polymerase or master mix. One of: q5, phusion, neb_taq, onetaq, vent, deepvent, longamp, primestar_max, kod_one, taq, pfu. Common product spellings are accepted (e.g. \"Q5 Hot Start\", \"KOD One\", \"PrimeSTAR Max\")." }, "forwardPrimer": { "type": "string", "residues": "nt", "description": "Forward primer, 5'→3'." }, "reversePrimer": { "type": "string", "residues": "nt", "description": "Reverse primer, 5'→3'." }, "highComplexityTemplate": { "type": "boolean", "default": false, "description": "Genomic or otherwise complex template. Where the vendor publishes a second, slower extension rate for one, it is used." } }, "additionalProperties": false }arguments 34 linesoligo_analysis unknown never probed
Full oligo analysis: nearest-neighbor Tm/ΔG/ΔH/ΔS plus hairpin and self-dimer screening with base-pair diagrams and warnings.
{ "type": "object", "required": [ "sequence" ], "properties": { "mgMM": { "type": "number", "default": 1.5, "description": "Divalent cation [Mg2+] (mM)." }, "naMM": { "type": "number", "default": 50, "description": "Monovalent cation [Na+]/[K+] (mM)." }, "dntpMM": { "type": "number", "default": 0.2, "description": "Total [dNTP] (mM), chelates Mg2+." }, "oligoNM": { "type": "number", "default": 250, "description": "Total strand concentration (nM)." }, "sequence": { "type": "string", "residues": "nt", "description": "Nucleotide sequence (raw or FASTA; IUPAC accepted)." } }, "additionalProperties": false }arguments 34 linesin_silico_pcr unknown never probed
Predict PCR products for a template and a pair of primers (IUPAC-aware, allows mismatches, handles circular templates). Primers may carry a non-templated 5' tail — a restriction site, a Gibson arm, a Kozak, a tag: a primer primes on its 3' end, and the tail is carried into the product rather than required to match. start/end are the TEMPLATE-derived span, `length` is the whole product including tails, and `features` marks which product bases came from the oligos (present only when there is a tail). Each end reports annealedLength and tailLength.
{ "type": "object", "required": [ "template" ], "properties": { "circular": { "type": "boolean", "default": false, "description": "Treat the template as circular (plasmid)." }, "template": { "type": "string", "residues": "nt", "description": "Nucleotide sequence (raw or FASTA; IUPAC accepted)." }, "forwardPrimer": { "type": "string", "residues": "nt", "description": "Primer 1, 5'→3'." }, "maxMismatches": { "type": "integer", "default": 0, "maximum": 10, "minimum": 0, "description": "Mismatches tolerated per primer (0–10)." }, "reversePrimer": { "type": "string", "residues": "nt", "description": "Primer 2, 5'→3' (order does not matter). Optional: one primer alone is accepted and reports the products it makes on its own — none, unless the template carries inverted sites it can prime from both ends." }, "maxProductLength": { "type": "integer", "default": 50000, "maximum": 500000, "minimum": 1, "description": "Ignore predicted products longer than this (bp). A SEARCH WINDOW, not a claim about what amplifies: whole-plasmid inverse PCR — the reaction a q5-style site_directed_mutagenesis design is run as — makes one product the size of the plasmid, so raise this for a construct over 50 kb. `suppressedByLength` in the response counts what the window discarded." } }, "additionalProperties": false }arguments 43 linesprimer_design unknown never probed
De-novo PCR primer design (Primer3-style penalty picker): enumerate and score candidate primer pairs against length/Tm/GC/3'-clamp/structure constraints.
{ "type": "object", "required": [ "template" ], "properties": { "mgMM": { "type": "number", "default": 1.5, "description": "Divalent cation [Mg2+] (mM)." }, "naMM": { "type": "number", "default": 50, "description": "Monovalent cation [Na+]/[K+] (mM)." }, "gcMax": { "type": "number", "default": 60 }, "gcMin": { "type": "number", "default": 40 }, "tmMax": { "type": "number", "default": 63 }, "tmMin": { "type": "number", "default": 57 }, "tmOpt": { "type": "number", "default": 60 }, "dntpMM": { "type": "number", "default": 0.2, "description": "Total [dNTP] (mM), chelates Mg2+." }, "lenMax": { "type": "integer", "default": 25, "maximum": 100, "minimum": 1 }, "lenMin": { "type": "integer", "default": 18 }, "lenOpt": { "type": "integer", "default": 20 }, "gcClamp": { "type": "integer", "description": "Consecutive G/C required at the very 3' end (Primer3's PRIMER_GC_CLAMP). Omitted or 0 means no requirement." }, "oligoNM": { "type": "number", "default": 250, "description": "Total strand concentration (nM)." }, "maxPolyX": { "type": "integer", "description": "Longest run of one base a primer may contain (Primer3's PRIMER_MAX_POLY_X). Omitted or 0 means no limit." }, "template": { "type": "string", "residues": "nt", "description": "Nucleotide sequence (raw or FASTA; IUPAC accepted)." }, "maxReturn": { "type": "integer", "default": 5, "description": "Number of best pairs to return." }, "targetEnd": { "type": "integer", "description": "1-based inclusive end of the target region (optional)." }, "tmMaxDiff": { "type": "number", "default": 3, "description": "Max Tm difference within a pair (°C)." }, "ampliconMax": { "type": "integer", "default": 1000 }, "ampliconMin": { "type": "integer", "default": 100 }, "targetStart": { "type": "integer", "description": "1-based inclusive start of a region the product must span (optional)." }, "excludedRegions": { "type": "array", "items": { "type": "object", "required": [ "start", "end" ], "properties": { "end": { "type": "integer" }, "start": { "type": "integer" } } }, "description": "Regions no primer may overlap, 1-based inclusive, as {start,end}. start > end is a region crossing the origin of a circular template." }, "minThreePrimeDG": { "type": "number", "description": "Floor on the NN ΔG37 (kcal/mol) of the five 3'-most bases; a more stable end than this is rejected. Deliberately not Primer3's max_end_stability, which is a different scale this model has not been calibrated against." } }, "additionalProperties": false }arguments 125 linesbarcode_audit unknown never probed
Take a set of barcodes and report the minimum edit distance in it, which pairs sit at that distance, any duplicates, the GC range and the longest homopolymer. The pairs are the point: 'minimum distance 2' is a number, and 'these two barcodes are one substitution apart' is something to fix. Use before committing a pool you inherited or assembled by hand — a single close pair makes two constructs indistinguishable in the data and nothing downstream can detect it.
{ "type": "object", "required": [ "barcodes" ], "properties": { "metric": { "enum": [ "levenshtein", "hamming" ], "type": "string", "default": "levenshtein", "description": "'levenshtein' counts substitutions, insertions and deletions — the right choice for nanopore or PacBio, and the safe default. 'hamming' counts substitutions only, which is faster and adequate when the platform's errors are substitutions (Illumina), but gives NO protection against an indel shifting one barcode into another." }, "barcodes": { "type": "string", "description": "The barcodes, as FASTA, one per line, or comma-separated. Max 1,000, because every pair is compared." } }, "additionalProperties": false }arguments 22 linesdna_molarity unknown never probed
Nucleic-acid quantity conversions: molar mass, amount (pmol/nmol), molar and mass concentration, and copy number, from mass ± volume and either a length or a sequence.
{ "type": "object", "required": [], "properties": { "type": { "enum": [ "dsDNA", "ssDNA", "ssRNA" ], "type": "string", "default": "dsDNA", "description": "Molecule type." }, "length": { "type": "integer", "default": 1000, "description": "Length in bp (dsDNA) or nt (ssDNA/ssRNA). Ignored when a sequence is given." }, "massNg": { "type": "number", "default": 100, "description": "Mass in nanograms." }, "sequence": { "type": "string", "residues": "nt", "description": "Optional sequence — overrides length and gives an exact molar mass from base composition." }, "volumeUl": { "type": "number", "default": 0, "description": "Volume in microlitres (0 = unknown; needed for concentration)." }, "targetUnit": { "enum": [ "nM", "uM", "ngPerUl" ], "type": "string", "default": "nM", "description": "Unit for targetConcentration." }, "targetVolumeUl": { "type": "number", "default": 20, "description": "Final volume of the diluted sample, in µL." }, "targetConcentration": { "type": "number", "description": "Optional: the concentration you need. Supplying it (with volumeUl, so there is a stock concentration to dilute FROM) returns a `dilution` plan — µL of stock and µL of diluent — instead of leaving C1V1 = C2V2 to be done by hand. The stock and the target may be quoted in different units; the molar mass converts between them." } }, "additionalProperties": false }arguments 56 linessite_directed_mutagenesis unknown never probed
Design site-directed mutagenesis primers (QuikChange overlapping or Q5 back-to-back) for a base substitution, an amino-acid codon swap, or an insertion/deletion/delins. The edit can be given as fields or, more simply, by NAME in `mutation`: "E52K", "p.Glu52Lys", "c.155A>G", "c.76_78del", "c.76_77insGGA", "c.76_78dup". A named mutation is checked against the template — if the reference allele it states is not what is actually at that position, the call is refused and the real base or residue is quoted back, because a coordinate belonging to a different transcript or the other strand yields perfectly well-formed primers for the wrong base. `interpretedAs` in the response says which reading was designed.
{ "type": "object", "required": [ "template" ], "properties": { "mgMM": { "type": "number", "default": 1.5, "description": "Divalent cation [Mg2+] (mM)." }, "naMM": { "type": "number", "default": 50, "description": "Monovalent cation [Na+]/[K+] (mM)." }, "style": { "enum": [ "quikchange", "q5" ], "type": "string", "default": "quikchange", "description": "Mutagenic primer style." }, "dntpMM": { "type": "number", "default": 0.2, "description": "Total [dNTP] (mM), chelates Mg2+." }, "insert": { "type": "string", "residues": "nt", "description": "Bases to put in place of the deleted span (delins edit). Omit for a pure deletion. NOTE the convention when deleteLength is 0: the insert lands immediately BEFORE `position`, so position 101 + insert \"GGA\" is the same edit as mutation: \"c.100_101insGGA\" — HGVS names the two flanking bases, this names the base the insert sits in front of. `interpretedAs` states which bases the insert ended up between." }, "newBase": { "enum": [ "A", "C", "G", "T" ], "type": "string", "description": "Replacement base (nt edit)." }, "oligoNM": { "type": "number", "default": 250, "description": "Total strand concentration (nM)." }, "residue": { "type": "integer", "description": "1-based residue number to change (aa edit)." }, "editKind": { "enum": [ "nt", "aa", "delins" ], "type": "string", "description": "Edit level. Normally omitted — it is inferred from the fields you send (newBase means nt, targetAa means aa, insert/deleteLength means delins)." }, "mutation": { "type": "string", "description": "The edit by name — \"E52K\", \"p.Glu52Lys\", \"Q100*\", \"c.155A>G\", \"A155G\", \"c.76_78del\", \"c.76_77insGGA\", \"c.76_78dup\", \"c.76delinsAA\". Replaces the field-by-field forms below. An unprefixed \"A123G\" is a legal reading at BOTH levels; it is resolved by which one matches the template, and refused if both do." }, "organism": { "enum": [ "ecoli", "human", "yeast", "cho", "pichia", "insect", "arabidopsis", "zebrafish" ], "type": "string", "default": "ecoli", "description": "Codon-usage table for choosing the new codon (aa edit). Latin names and common strain/cell-line names are accepted." }, "position": { "type": "integer", "description": "1-based position to substitute (nt), or the first base of the span to replace (delins). Required for those forms — it is never assumed. For a pure insertion (deleteLength 0) it is the base the insert goes in FRONT of." }, "targetAa": { "type": "string", "description": "Target amino acid, one-letter code incl '*' (aa edit)." }, "template": { "type": "string", "residues": "nt", "description": "Nucleotide sequence (raw or FASTA; IUPAC accepted)." }, "frameStart": { "type": "integer", "default": 1, "description": "1-based position of the first base of codon 1. Needed whenever the coding sequence does not start at base 1 of the template — a residue number means nothing without it." }, "armTmTarget": { "type": "number", "default": 60, "description": "Target Tm (°C) for each template-binding arm." }, "deleteLength": { "type": "integer", "description": "Template bases to remove, starting at `position` (delins edit). 0 with `insert` set is a pure insertion, placed immediately before `position`." } }, "additionalProperties": false }arguments 112 linesoligo_pool_screen unknown never probed
Screen a whole set of oligos you already have — every pair for cross-dimers, every oligo for its own hairpin and self-dimer, and the set for duplicates and Tm spread — and get back the conflicts ranked rather than a table of every combination. This is the pool-level answer cross_dimer gives one pair at a time: 51 primers is 1,275 pairs, which is 1,275 separate calls done by hand and one call done here. Not to be confused with multiplex_panel_design, which DESIGNS primers from templates; this takes the primers you have already ordered. A pairing that involves an oligo's 3' END is judged at a weaker ΔG than one that only pairs internally, because that end is where extension starts — the same two-bar rule the multiplex panel designer uses. Every number is a nearest-neighbor calculation over the sequences supplied, not a prediction of what the reaction will do.
{ "type": "object", "required": [], "properties": { "mgMM": { "type": "number", "default": 1.5, "description": "Divalent cation [Mg2+] (mM)." }, "naMM": { "type": "number", "default": 50, "description": "Monovalent cation [Na+]/[K+] (mM)." }, "fasta": { "type": "string", "residues": "nt", "description": "The pool as a FASTA paste (headers become the names), or as one sequence per line — which is what comes out of a spreadsheet column. An alternative to `oligos`." }, "dntpMM": { "type": "number", "default": 0.2, "description": "Total [dNTP] (mM), chelates Mg2+." }, "oligos": { "type": "array", "items": { "type": "object", "required": [ "sequence" ], "properties": { "name": { "type": "string", "description": "Label used throughout the result. Defaults to oligo_1, oligo_2, …" }, "sequence": { "type": "string", "description": "The oligo, 5'→3'." } } }, "description": "The pool, as objects with a name and a sequence. Up to 384. Use this or `fasta`, not both." }, "oligoNM": { "type": "number", "default": 250, "description": "Total strand concentration (nM)." }, "maxConflicts": { "type": "integer", "default": 200, "description": "Conflict rows returned, most stable first. The COUNTS are always complete." }, "internalThresholdDG": { "type": "number", "default": -9, "description": "The looser bar for a pairing that only sequesters primer internally, away from either 3' end." }, "threePrimeThresholdDG": { "type": "number", "default": -6, "description": "ΔG (kcal/mol) at or below which a pairing that involves a 3' END counts as a conflict." } }, "additionalProperties": false }arguments 67 linescross_dimer unknown never probed
Screen two oligos for the most stable heterodimer (cross-dimer) between them.
{ "type": "object", "required": [ "sequenceA", "sequenceB" ], "properties": { "sequenceA": { "type": "string", "residues": "nt", "description": "First oligo (5'→3')." }, "sequenceB": { "type": "string", "residues": "nt", "description": "Second oligo (5'→3')." } }, "additionalProperties": false }arguments 20 linesprimer_specificity unknown never probed
Self-hosted e-PCR-style screen for off-target amplicons predicted by a primer pair against a small set of curated reference genomes (currently: E. coli K-12 MG1655, B. subtilis 168, human mitochondrion rCRS, Mycoplasma hyorhinis SK76 — see genomesChecked in the response for the exact list, and note that the nuclear human and mouse genomes are NOT covered). Amplicons are 1-based inclusive on the plus strand; a product across a circular genome's origin reports an end lower than its start and sets wraps: true. This checks background/host-genome specificity, NOT whether the primers hit your intended target — pair it with in_silico_pcr against your own template for that. Each off-target end reports its 3' ANCHOR — the primer's unbroken run of matched bases at the extending end — with that anchor's nearest-neighbor ΔG and a margin against the intended, fully matched reaction, so a site can be told apart by WHERE its mismatches fall rather than only how many there are: one mismatch at the 5' end leaves a site nearly as strong, and one at the 3' base leaves it unable to prime at all. Batchable over candidate REVERSE primers against one fixed forward primer (screen many candidates against a shared partner) — not independent primer-pair batching, which this tool doesn't support. A primer may carry a non-templated 5' tail (a restriction site, a Gibson arm, a tag): the screen looks for a 3'-anchored annealing region as well as a full-length match, so a tailed cloning primer is screened rather than silently matching nothing. Each end's `anchor` is the annealed run, which is the length that matters for extension, and `start`/`end` are measured on the ANNEALED footprints — the bases each primer actually pairs with on the genome — so `length` (the product, tails included) equals end - start + 1 only for untailed primers. Screening a TAILED primer without `intendedTemplate` inflates every margin by the tail's own free energy, because nothing about an oligo says where its non-templated part ends; `intended.basis` reports which footprint the margins rest on.
{ "type": "object", "required": [ "forwardPrimer", "reversePrimer" ], "properties": { "forwardPrimer": { "type": "string", "residues": "nt", "description": "Forward primer, 5'→3'." }, "maxMismatches": { "type": "integer", "default": 1, "maximum": 4, "minimum": 0, "description": "Mismatches tolerated per primer against a reference genome. Capped at 4 — past that a primer would not extend anyway. No primer length is refused for raising this: the pigeonhole seed just gets shorter and less selective, so more candidate sites are verified and the call takes longer (an 18-mer over the bundled genomes runs in ~0.1 s at 0 and ~1.5 s at 4). A short primer at a high setting can still exceed the binding-site pairing limit and come back \"unsupported\" — a 13-mer at 4 binds too many places to pair up, where an 18-mer screens fine — and either primer under 13 nt is not screened at all (ambiguousSeed: true, no amplicons)." }, "reversePrimer": { "type": "string", "residues": "nt", "description": "Reverse primer, 5'→3'." }, "intendedTemplate": { "type": "string", "residues": "nt", "description": "The template these primers are meant to amplify. Only their annealing footprints are read from it, so an amplicon, a plasmid or a cassette is always enough (at most 1,000,000 bp). Passing it is what makes closestCompetitorMargin true for a primer carrying a 5' tail: a tail is non-templated by definition, so nothing about the oligo says where it ends, and without a template the screen has to assume the whole oligo anneals — which credits the intended reaction with a duplex the tail cannot form ANYWHERE and inflates every margin by that tail's own free energy. Searched on both strands as given; a primer that cannot be found on it is an error rather than a silent fall back to the whole oligo." }, "maxProductLength": { "type": "integer", "default": 5000, "minimum": 1, "description": "Ignore candidate off-target products longer than this (bp) — a search-window cap, not a biological claim." } }, "additionalProperties": false }arguments 38 linesoligo_cofold unknown never probed
Minimum-free-energy structure and ΔG for one oligo (hairpin) or two oligos together (homo/heterodimer), using ViennaRNA's published loop model at a temperature you choose — DNA parameters (Mathews 2004) by default, RNA (Turner 2004) on request. Reports each strand alone, the duplex, and the interaction ΔG the two gain by pairing with each other rather than folding alone, which is the number a primer-dimer screen wants. Unlike oligo_analysis's fast stack-sum screen this is a full loop model with bulge, internal-loop and dangling-end terms; the two are on different parameter sets and must not be compared. PREDICTED, NOT MEASURED. No skill statistic is claimed for predicting whether a PCR fails. Loop-model MFE folding reproduces measured structure well for short duplexes and progressively worse with length; the ΔG itself carries roughly kcal/mol-scale uncertainty and the MFE structure is one structure out of an ensemble — request `partition` for the ensemble free energy, which is the more honest single number when several structures compete. Valid for: short oligos, at most 200 nt per strand, at the temperature given. It models two strands in isolation at no particular concentration: it does not know your primer concentration, salt, or cycling program, so it cannot say whether a dimer will actually form in your tube.
{ "type": "object", "required": [ "a" ], "properties": { "a": { "type": "string", "maxLength": 800, "description": "First oligo, 5'→3'. Max 200 nt." }, "b": { "type": "string", "maxLength": 800, "description": "Second oligo. Omit to analyze hairpin structure in 'a' alone; pass the same sequence as 'a' for a homodimer." }, "alphabet": { "enum": [ "dna", "rna" ], "type": "string", "default": "dna", "description": "Which measured parameter set to use. This is not cosmetic — the same 20-mer can differ by several kcal/mol between them." }, "partition": { "type": "boolean", "default": false, "description": "Also compute the ensemble free energy over all structures, not just the MFE one. Costs a second pass." }, "temperature": { "type": "number", "default": 37, "maximum": 120, "minimum": -20, "description": "°C. Primer dimers matter at the annealing temperature, not at 37 °C." } }, "additionalProperties": false }arguments 40 linesrestriction_sites unknown never probed
Find restriction enzyme recognition sites in a DNA sequence.
{ "type": "object", "required": [ "sequence" ], "properties": { "enzymes": { "type": "array", "items": { "type": "string" }, "description": "Enzyme names to scan; omit to scan the curated common-enzyme set. A name is resolved against the curated set, the Type IIS cutters and the generated REBASE table, case-, punctuation- and HF/v2-variant-insensitively, so \"ecori\", \"EcoRI-HF\", \"BsaI\" and \"BsmFI\" all resolve. A name that resolves to nothing is REJECTED rather than dropped — an unscanned enzyme reported as having no sites is indistinguishable from one that genuinely does not cut." }, "circular": { "type": "boolean", "default": false, "description": "Treat the sequence as circular (plasmid) so sites spanning the origin are found." }, "sequence": { "type": "string", "residues": "nt", "description": "Nucleotide sequence (raw or FASTA; IUPAC accepted)." } }, "additionalProperties": false }arguments 26 linescloning_simulate unknown never probed
Assemble fragments by Gibson/overlap, Golden Gate (Type IIS), restriction–ligation (sticky or blunt), TOPO/TA, LIC or SLIC (T4-polymerase chew-back) or In-Fusion/CPEC, returning the product, the junctions and — for the primer-design methods — the junction primers. Each method is modeled as its own chemistry rather than as one product model with different labels: LIC's chew-back stops at the first occurrence of the single dNTP supplied, so a tail carrying that base stops it early and a tail without one lets it run past the junction, and both are refused with the offending base and position named.
{ "type": "object", "required": [ "method" ], "properties": { "names": { "type": "array", "items": { "type": "string" }, "description": "Optional labels for each fragment." }, "enzyme": { "type": "string", "default": "BsaI", "description": "Type IIS enzyme for Golden Gate — one of BsaI, BbsI, Esp3I (BsmBI); \"BsmBI\" also resolves to Esp3I. Any other name is rejected rather than substituted." }, "insert": { "type": "string", "residues": "nt", "description": "Insert sequence (restriction, topo and lic methods)." }, "method": { "enum": [ "gibson", "goldengate", "restriction", "topo", "lic", "slic", "infusion" ], "type": "string", "default": "gibson", "description": "Assembly method. gibson/goldengate design the junction primers for bare fragments; restriction and topo build a product from a vector and an insert; lic and slic model T4-polymerase chew-back (sequence-defined and time-stopped respectively); infusion is In-Fusion/CPEC, 15 bp terminal homology with no exonuclease, and works out the fragment ORDER for itself." }, "vector": { "type": "string", "residues": "nt", "description": "Vector sequence (restriction, topo and lic methods; for lic, the LINEARIZED vector)." }, "enzyme3": { "type": "string", "default": "BamHI", "description": "Insert 3′ enzyme (restriction method)." }, "enzyme5": { "type": "string", "default": "EcoRI", "description": "Insert 5′ enzyme (restriction method)." }, "circular": { "type": "boolean", "default": true, "description": "Produce a circular product." }, "topoMode": { "enum": [ "ta", "blunt", "directional" ], "type": "string", "default": "ta", "description": "TOPO chemistry (topo method): TA (Taq 3′-A), blunt, or directional (pENTR/D-TOPO, needs 5′-CACC on the insert)." }, "fragments": { "type": "array", "items": { "type": "string" }, "maxItems": 24, "description": "Fragments (5′→3′). Used by gibson/goldengate/slic/infusion. gibson and goldengate assemble them head-to-tail in the order given and add the junctions by primer; slic needs the homology already ON the fragments and keeps the order given; infusion needs it on the fragments too but derives the order from the homologies, so the order listed here is ignored. slic and infusion take at most 24." }, "overlapLen": { "type": "integer", "default": 20, "description": "Gibson homology-arm length (bp)." }, "armTmTarget": { "type": "number", "default": 60, "description": "Target annealing Tm (°C) for primer arms." }, "chewBackLen": { "type": "integer", "default": 0, "minimum": 0, "description": "slic method: nucleotides removed from each 3′ end. A SLIC chew-back has no dNTP to arrest it and is stopped by time, so this is an input rather than a property of the sequence. 0 (default) models the intended reaction — chewed to the full homology and no further; any positive value is checked against each junction's own homology, and both overrunning it and falling short of meeting the chew-back coming the other way are reported." }, "homologyLen": { "type": "integer", "default": 15, "minimum": 15, "description": "infusion method: terminal homology required at every junction, in bp. At least 15 — the junction is annealed and extended by a polymerase with no exonuclease to widen it and no ligase to seal it, so a shorter overlap is a different chemistry rather than a weaker version of this one." }, "vectorEnzyme3": { "type": "string", "description": "Vector 3′ enzyme (restriction method); defaults to enzyme3." }, "vectorEnzyme5": { "type": "string", "description": "Vector 5′ enzyme (restriction method); defaults to enzyme5. Set a different, compatible enzyme (e.g. BglII for a BamHI insert) to model heterologous-overhang cloning." }, "insertNucleotide": { "enum": [ "A", "C", "G", "T" ], "type": "string", "description": "lic method: the single dNTP the INSERT's chew-back was run with. Normally the COMPLEMENT of vectorNucleotide (the classic pair is dTTP on the vector, dATP on the insert) — with the same base for both, each junction's shared block would have to avoid that base and its complement at once." }, "vectorNucleotide": { "enum": [ "A", "C", "G", "T" ], "type": "string", "description": "lic method: the single dNTP the VECTOR's chew-back was run with (T for dTTP…). Required — T4 pol's exonuclease stops at the first occurrence of this base reading inward from each 3′ end, so there is no answer without it." }, "mergePreAddedArms": { "type": "boolean", "default": true, "description": "Gibson only. When two fragments already share terminal sequence, count that share ONCE (the default — it is a homology arm the fragments already carry) or set false to concatenate it twice. The second reading is the right one when the shared block is a genuine tandem repeat, e.g. a 2x tag or enhancer split between its copies: nothing in the two fragments can tell the two apart, so the choice belongs to the caller. Either way the share is reported in preAddedArms and both readings are returned in `readings`." }, "dephosphorylateVector": { "type": "boolean", "default": false, "description": "CIP/rSAP-dephosphorylate the vector to suppress self-ligation background (restriction method)." } }, "additionalProperties": false }arguments 138 linesplasmid_annotate unknown never probed
Auto-detect common cloning features (promoters, tags, origins, resistance markers, MCS, primers) on both strands. Signatures under 20 bp must match exactly; longer ones tolerate up to ~10% mismatches so point mutants still annotate — each feature reports its own `mismatches` count and an `exact` flag.
{ "type": "object", "required": [ "sequence" ], "properties": { "sequence": { "type": "string", "residues": "nt", "description": "Nucleotide sequence (raw or FASTA; IUPAC accepted)." } }, "additionalProperties": false }arguments 14 linesconstruct_qc unknown never probed
Lint a coding DNA sequence for premature stops, internal RBS/polyA motifs, unwanted restriction sites, GC extremes and repeats.
{ "type": "object", "required": [ "sequence" ], "properties": { "gcLow": { "type": "number", "default": 30, "description": "GC% below this flags an AT-rich window." }, "gcHigh": { "type": "number", "default": 70, "description": "GC% above this flags a GC-rich window." }, "gcWindow": { "type": "integer", "default": 50, "description": "Sliding-window size (nt) for GC-extreme scanning." }, "sequence": { "type": "string", "residues": "nt", "description": "Nucleotide sequence (raw or FASTA; IUPAC accepted)." }, "frameStart": { "type": "integer", "default": 1, "description": "1-based nucleotide where the reading frame begins." }, "avoidEnzymes": { "type": "array", "items": { "type": "string" }, "description": "Enzyme names whose internal sites should be flagged as errors. Matched against the curated common-enzyme set plus the Golden Gate Type IIS enzymes (BsaI, BbsI, Esp3I/BsmBI); an unrecognized name is rejected, never skipped." }, "homopolymerMin": { "type": "integer", "default": 8, "description": "Minimum run length to flag a homopolymer." }, "crypticOrfMinAa": { "type": "integer", "default": 20, "description": "Minimum peptide length (aa) for a hidden alternate-frame ORF to be flagged." } }, "additionalProperties": false }arguments 51 linesconstruct_autofix unknown never probed
Iteratively substitutes synonymous codons to resolve unwanted restriction sites (domestication for Golden Gate), homopolymers, tandem repeats, predicted secondary structure, cryptic RBS/polyA motifs and hidden alternate-frame ORFs that construct_qc flags — without changing the encoded protein (verified). Does NOT touch premature stops or GC extremes; re-run construct_qc afterward to confirm. A native TypeScript alternative to a constraint-solver sidecar.
{ "type": "object", "required": [ "sequence" ], "properties": { "gcLow": { "type": "number", "default": 30 }, "gcHigh": { "type": "number", "default": 70 }, "gcWindow": { "type": "integer", "default": 50 }, "organism": { "enum": [ "ecoli", "human", "yeast", "cho", "pichia", "insect", "arabidopsis", "zebrafish" ], "type": "string", "default": "ecoli", "description": "Codon-usage table to prefer among synonymous options." }, "sequence": { "type": "string", "residues": "nt", "description": "Nucleotide sequence (raw or FASTA; IUPAC accepted)." }, "maxPasses": { "type": "integer", "default": 3, "maximum": 10, "minimum": 1, "description": "Repeat full passes until clean or no further progress." }, "frameStart": { "type": "integer", "default": 1, "description": "1-based nucleotide where the reading frame begins." }, "avoidEnzymes": { "type": "array", "items": { "type": "string" }, "description": "Enzyme names whose internal sites should be removed (e.g. [\"BsaI\",\"BsmBI\"] for Golden Gate domestication)." }, "homopolymerMin": { "type": "integer", "default": 8 }, "crypticOrfMinAa": { "type": "integer", "default": 20, "description": "Minimum peptide length (aa) for a hidden alternate-frame ORF to be flagged." } }, "additionalProperties": false }arguments 69 linessanger_indel_spectrum unknown never probed
Quantify CRISPR editing from a pair of Sanger traces — an unedited control and the edited pool — by decomposing the edited trace onto shifted copies of the control. Returns the indel spectrum (how much of the pool carries each insertion or deletion size), the unedited fraction, and the R² of the decomposition, which is the number that says whether the model fits your traces at all. Non-negative least squares, so no allele is ever assigned a negative share. Does not work for base editing, which makes a mixed base rather than a shift. PREDICTED, NOT MEASURED. Every run reports its own R²: how much of the observed window the shifted-control basis actually explains. That is a measured adequacy of the model on YOUR traces, and a low value means the assumption is wrong here rather than that the edit is weak. On accuracy against a reference method for real samples, none is published for this implementation — the underlying decomposition is TIDE's, whose authors report their own concordance with amplicon sequencing, and that number does not transfer to this code so it is not quoted. This implementation's exact recovery of synthetic mixtures is deliberately not offered as validation either: it tests the arithmetic, not whether the model fits a real trace. Valid for: A pool of alleles that differ from one control read by simple insertions or deletions at a known cut site, where both reads come from the same amplicon and chemistry and both extend well past the cut. NOT valid for substitution-only edits — base editing produces a mixed base, not a shift, and this model cannot see it — nor for a knock-in whose insert is novel sequence rather than a frame shift of the control, nor for any run whose R² comes back low.
{ "type": "object", "required": [ "controlBases", "controlChannels", "editedBases", "editedChannels", "cutPosition" ], "properties": { "guard": { "type": "number", "default": 3, "description": "Bases skipped immediately after the cut, where the trace is least reliable." }, "offset": { "type": "number", "description": "Override the alignment offset between the reads. By default it is found from the base calls upstream of the cut, which is reported back along with the identity achieved." }, "maxIndel": { "type": "number", "default": 10, "description": "Largest indel to include in the basis, in bp (max 20). Every shift from −maxIndel to +maxIndel is fitted." }, "cutPosition": { "type": "number", "description": "1-based position of the expected cut, in CONTROL read coordinates." }, "editedBases": { "type": "string", "residues": "nt", "description": "Base calls of the edited pool's read." }, "controlBases": { "type": "string", "residues": "nt", "description": "Base calls of the UNEDITED control read." }, "windowLength": { "type": "number", "default": 70, "description": "Bases downstream of the cut used for the decomposition (20-300). Longer is better conditioned but needs more clean read." }, "editedChannels": { "type": "array", "items": { "type": "array", "items": { "type": "number" } }, "description": "Per-base [A, C, G, T] intensities of the edited read, same convention." }, "controlChannels": { "type": "array", "items": { "type": "array", "items": { "type": "number" } }, "description": "Per-base [A, C, G, T] intensities of the control read, one row per called base, read at that base's peak location (trace arrays are indexed by scan, not by base)." } }, "additionalProperties": false }arguments 66 linesvirtual_gel unknown never probed
Predict restriction-digest fragment sizes and their gel migration positions against a chosen DNA ladder.
{ "type": "object", "required": [ "sequence" ], "properties": { "ladder": { "enum": [ "1 kb", "1 kb Plus", "100 bp" ], "type": "string", "default": "1 kb", "description": "DNA ladder to plot alongside the sample lane." }, "enzymes": { "type": "array", "items": { "type": "string" }, "description": "Enzyme names to digest with, from the curated common-enzyme set (see restriction_sites for the full list). An unrecognized name is rejected rather than skipped, so an empty band pattern always means \"no sites\"." }, "circular": { "type": "boolean", "default": false, "description": "Treat the sequence as circular (plasmid)." }, "sequence": { "type": "string", "residues": "nt", "description": "Nucleotide sequence (raw or FASTA; IUPAC accepted)." } }, "additionalProperties": false }arguments 36 linesligation_setup unknown never probed
Work out how many microlitres of vector and insert to pipette to hit a target molar ratio, from each part's length and stock concentration. Handles one insert or several with independent equivalents (Gibson, Golden Gate, MoClo), reports pmol and ng per part alongside the volumes, and flags the two things that actually go wrong on a bench: a volume below what a pipette measures reliably, and a plan whose DNA does not leave room for buffer and enzyme. A molar ratio is about moles, so a shorter insert at 3 molar equivalents goes in at LESS mass than the vector — that conversion is the point.
{ "type": "object", "required": [ "vectorLengthBp", "vectorNgPerUl" ], "properties": { "inserts": { "type": "array", "items": { "type": "object", "required": [ "lengthBp", "ngPerUl" ], "properties": { "label": { "type": "string" }, "ngPerUl": { "type": "number" }, "lengthBp": { "type": "integer" }, "equivalents": { "type": "number", "default": 1 } } }, "description": "Multi-fragment assembly: one entry per insert, each with its own length, stock and molar equivalents. Overrides insertLengthBp/insertNgPerUl/molarRatio when present." }, "vectorNg": { "type": "number", "default": 50, "description": "How much backbone to put in the reaction, ng. This is the quantity you fix; every insert mass follows from the ratio." }, "molarRatio": { "type": "number", "default": 3, "description": "Molar equivalents of insert per vector. 3 is the usual starting point for a sticky-end ligation; 1-2 is common for Gibson and Golden Gate." }, "insertNgPerUl": { "type": "number", "description": "Insert stock concentration, ng/µL." }, "vectorNgPerUl": { "type": "number", "description": "Backbone stock concentration, ng/µL." }, "insertLengthBp": { "type": "integer", "description": "Insert length in bp. Use `inserts` instead for a multi-fragment assembly." }, "vectorLengthBp": { "type": "integer", "description": "Backbone length in bp." }, "vectorSequence": { "type": "string", "residues": "nt", "description": "Optional backbone sequence — gives an exact molar mass from base composition instead of the 650 g/mol/bp average." }, "reactionVolumeUl": { "type": "number", "default": 20, "description": "Total reaction volume, µL." } }, "additionalProperties": false }arguments 72 linesgolden_gate_from_parts unknown never probed
Golden Gate as the reaction runs: digest pre-domesticated part plasmids with a Type IIS enzyme and assemble them in the order their OVERHANGS dictate. The fragment released from each part is the one carrying no recognition site (the site goes out with the backbone, which is why a mis-ordered assembly is not re-cut), and the assembly order is an OUTPUT — a set whose overhangs do not close into a single cycle has no product, and the reason is the answer. Distinct from cloning_simulate's `goldengate` method, which does the other job: designing the primers that ADD the sites to BARE parts, assembled in the order you list them.
{ "type": "object", "required": [ "parts" ], "properties": { "parts": { "type": "array", "items": { "type": "object" }, "maxItems": 24, "minItems": 2, "description": "The part plasmids: [{ name, sequence, circular }]. Each needs two Type IIS sites facing INWARDS at the part. `circular` defaults to true, which is what a level-0 part plasmid is. 2-24 parts, each at most 30,000 bp and 200,000 bp in total." }, "enzyme": { "enum": [ "BsaI", "BsmBI", "BbsI", "SapI" ], "type": "string", "default": "BsaI", "description": "Type IIS enzyme (BsaI, BsmBI, BbsI, SapI). NEB's variant names (BsaI-HFv2, BbsI-HF, BsmBI) fold to the parent enzyme; any other name is rejected rather than substituted, since site, spacer and overhang length are all enzyme-specific." } }, "additionalProperties": false }arguments 29 linesband_traceback unknown never probed
Explain a band you measured on a gel. Given the template, both primers and the observed size, it enumerates every pair of priming sites — including a single primer priming both strands — that would give a product that size, and ranks them by how much of each primer's 3' end matches without interruption, which is what decides whether a mispriming event can extend at all. Reports no yield and assigns no share of the band: the band is the input, not the output. Says plainly when nothing on this template explains the size, and what that points to instead.
{ "type": "object", "required": [ "template", "forwardPrimer", "reversePrimer", "observedSize" ], "properties": { "circular": { "type": "boolean", "default": false, "description": "Template is circular (a plasmid)." }, "template": { "type": "string", "residues": "nt", "description": "The template you amplified, raw or FASTA. Max 200,000 bp." }, "toleranceBp": { "type": "number", "description": "Override the tolerance with a fixed window in bp." }, "observedSize": { "type": "number", "description": "The band size you measured off the gel, in bp." }, "forwardPrimer": { "type": "string", "residues": "nt", "description": "Forward primer, 5'→3'." }, "maxCandidates": { "type": "number", "default": 40, "description": "Cap on returned candidates, best-anchored first." }, "maxMismatches": { "type": "number", "default": 3, "description": "Mismatches tolerated per primer while looking for sites (max 6). Higher finds more explanations and more coincidences." }, "reversePrimer": { "type": "string", "residues": "nt", "description": "Reverse primer, 5'→3'." }, "tolerancePercent": { "type": "number", "default": 10, "description": "How far off the size read may be, as a percentage. A percentage rather than a fixed number of bases because ±10% of 200 bp is not the same reading precision as ±10% of 5 kb." } }, "additionalProperties": false }arguments 55 linesassembly_outcomes unknown never probed
Enumerate the specific wrong plasmids a multi-part Golden Gate or Gibson assembly can produce — a part dropped, inverted, duplicated, two parts swapped, the backbone self-circularized — as full sequences, ranked by how few independent mis-ligations each needs. Golden Gate outcomes are annotated with the MEASURED overhang cross-talk they would have to exploit (Potapov/Pryor ligation data). Feed the result to diagnostic_digest to pick a screening enzyme. Reports no probability per outcome: the ligation data does not measure transformation or vector background.
{ "type": "object", "required": [ "fragments" ], "properties": { "names": { "type": "array", "items": { "type": "string" }, "description": "Optional labels for the parts, in the same order (\"backbone\", \"promoter\", \"CDS\"). Used in every outcome label." }, "enzyme": { "type": "string", "default": "BsaI", "description": "Golden Gate only — the Type IIS enzyme, which fixes the overhang length (BsaI, BbsI, Esp3I (BsmBI))." }, "method": { "enum": [ "goldengate", "gibson" ], "type": "string", "default": "goldengate", "description": "How the parts are joined. Golden Gate junctions are the Type IIS fusion overhangs; Gibson junctions are the homology arms." }, "dataset": { "enum": [ "generic-t4-37c-1h", "bsai-hfv2" ], "type": "string", "default": "generic-t4-37c-1h", "description": "Which ligation dataset to read overhang cross-talk from (Golden Gate only)." }, "circular": { "type": "boolean", "default": true, "description": "Circular product. Only circular assemblies are covered — a linear product's leading end is a free terminus, not a junction." }, "fragments": { "type": "array", "items": { "type": "string" }, "description": "The parts in assembly order, raw or FASTA — the same list cloning_simulate takes. 2-8 parts." }, "overlapLen": { "type": "number", "default": 20, "description": "Gibson only — homology arm length, which must match what the assembly was designed with." }, "maxAlternatives": { "type": "number", "default": 12, "description": "Cap on returned alternatives, most accessible first. The pre-cap count is always reported as alternativesEnumerated." } }, "additionalProperties": false }arguments 61 linesdiagnostic_digest unknown never probed
Pick the restriction digest that tells your intended construct apart from the wrong ones on a screening gel. Digests every candidate, works out which bands would actually resolve at the chosen agarose percentage (size ratio, the gel's resolving window, and whether a band is too faint to score), and ranks single enzymes — then buffer-checked pairs if no single one works. The criterion is separating the INTENDED construct from every alternative; telling the alternatives apart from each other is reported as a bonus. Get the alternatives from assembly_outcomes.
{ "type": "object", "required": [ "intended", "alternatives" ], "properties": { "enzymes": { "type": "array", "items": { "type": "string" }, "description": "Restrict the search to these enzymes (e.g. the ones on your bench). Default is the whole curated set of 49. An unrecognized name is rejected rather than skipped, so \"does not discriminate\" always means it was actually tried." }, "circular": { "type": "boolean", "default": true, "description": "Treat every candidate as a circular plasmid." }, "intended": { "type": "string", "residues": "nt", "description": "The construct you designed, raw or FASTA." }, "alternatives": { "type": "array", "items": { "type": "object", "required": [ "sequence" ], "properties": { "label": { "type": "string", "description": "What this wrong construct is (\"empty vector\", \"insert reversed\")." }, "sequence": { "type": "string", "description": "Its full sequence, raw or FASTA." } } }, "description": "The wrong constructs to screen against, 1-12. assembly_outcomes emits these ready-made as `forDiagnosticDigest`." }, "includePairs": { "enum": [ "auto", "always", "never" ], "type": "string", "default": "auto", "description": "Whether to search double digests. \"auto\" adds them only when no single enzyme separates everything." }, "agarosePercent": { "type": "number", "default": 1, "description": "Agarose percentage of the screening gel. Snapped to the nearest tabulated value (0.5, 0.7, 1, 1.2, 1.5, 2) and the one used is reported back, since the resolving window is what decides which bands separate." }, "maxSuggestions": { "type": "number", "default": 5, "description": "How many ranked options to return." } }, "additionalProperties": false }arguments 67 linespromoter_predict unknown never probed
Scan DNA for E. coli sigma-70 promoters and estimate each one's transcription initiation rate, with the free-energy terms it is built from: the -35 and -10 boxes, the spacer, the discriminator, the extended -10 and the initial transcribed region. Pairs with rbs_predict — together they separate 'nothing is transcribed' from 'it is transcribed and not translated', which no single measurement on the sequence does. Both strands by default, because a promoter reading into your insert from the other strand is still a promoter. PREDICTED, NOT MEASURED. R^2 = 0.45 and 0.60 against the two INDEPENDENT in vivo datasets the authors tested (Hossain et al., 4,350 promoters, Spearman rho = 0.69; Urtecho et al., 10,898 promoters, rho = 0.67). The widely quoted R^2 = 0.80 is a held-out tenth of the authors' OWN in vitro transcription data and is not the number to plan against: a promoter in a cell is the in vivo case, where between a third and a half of the variance is unexplained. Valid for: sigma-70 (housekeeping) promoters in E. coli. NOT valid for another sigma factor, another organism, a promoter under activator or repressor control, or anything about mRNA stability or translation — rbs_predict is the translation half, and neither speaks to the other.
{ "type": "object", "required": [ "sequence" ], "properties": { "limit": { "type": "number", "default": 10, "maximum": 100, "minimum": 1, "description": "How many of the strongest promoters to return." }, "sequence": { "type": "string", "description": "DNA to scan, 80-10000 nt. A promoter region, a 5' UTR with its upstream context, or a whole cassette." }, "bothStrands": { "type": "boolean", "default": true, "description": "Scan the reverse strand too. Leave on unless you know the orientation — cryptic antisense promoters are a common and easily missed cause of trouble." } }, "additionalProperties": false }arguments 25 linesrepeat_instability unknown never probed
Find the exact direct repeats in a construct that make it deletable, and build the molecule each pair would collapse to. Two copies of the same terminator or promoter in a multi-gene assembly let the DNA between them recombine out — silently, so the clone grows and the map looks right until it is sequenced. Returns each repeat pair's coordinates plus the resulting sequence(s), ordered by repeat length and spacer, the two factors that govern how readily a pair recombines. Reports no deletion RATE: none is derivable from sequence alone. Feed a deletion product to diagnostic_digest to screen for it.
{ "type": "object", "required": [ "sequence" ], "properties": { "circular": { "type": "boolean", "default": true, "description": "Treat as a plasmid. A circular construct is searched across its own arbitrary start, so a repeat straddling position 1 is not missed, and each pair reports BOTH circles the recombination makes." }, "maxPairs": { "type": "number", "default": 60, "description": "Cap on reported pairs, most recombinogenic first. The pre-cap count is always reported as pairsFound." }, "sequence": { "type": "string", "residues": "nt", "description": "The construct, raw or FASTA. Max 500,000 bp." }, "minRepeatLength": { "type": "number", "default": 20, "description": "Shortest repeat to report, in bp (default 20). Below about 20 bp homologous recombination has little to work with and chance matches multiply." }, "includeSequences": { "type": "boolean", "default": true, "description": "Return the full product sequences. Turn off for a coordinates-only summary over a large construct." } }, "additionalProperties": false }arguments 34 linesnonrepetitive_parts_find unknown never probed
Given a toolbox of genetic parts, return the largest subset in which no two parts share more than a chosen length of sequence — on either strand. Parts that share a long stretch recombine into each other in a multi-part assembly and are the single largest cause of DNA synthesis failure, and neither shows up when the parts are checked one at a time. Reports every conflicting pair and why each dropped part was dropped. Deterministic: no model, no rate, no score. Use nonrepetitive_parts_design to build new parts instead of selecting from existing ones.
{ "type": "object", "required": [ "parts" ], "properties": { "lmax": { "type": "integer", "default": 15, "maximum": 40, "minimum": 8, "description": "Longest stretch two parts may share, in bp (default 15). Two parts conflict when they share MORE than this. Below 8 bp every pair of sequences matches by chance." }, "parts": { "type": "string", "description": "The toolbox as (multi-)FASTA — each record's header becomes the part's name. Max 4,000 parts, 5,000 bp each." }, "strategy": { "enum": [ "2apx", "greedy" ], "type": "string", "default": "2apx", "description": "Which approximation picks the subset. Maximum independent set is NP-hard, so neither is guaranteed largest: '2apx' is the standard 2-approximation, 'greedy' repeatedly drops the most-conflicting part. Try both — they disagree on real toolboxes." }, "bothStrands": { "type": "boolean", "default": true, "description": "Count a shared stretch even when one part carries it reverse-complemented. Recombination and synthesis both see both strands, so leaving this on is almost always right." } }, "additionalProperties": false }arguments 34 linesnonrepetitive_parts_design unknown never probed
Build a set of new genetic parts that match a degenerate (IUPAC) template and share more than a chosen length with nothing — not each other, not themselves, not a background sequence you supply. This is how a toolbox of promoters, RBSs, terminators or sgRNA handles is made large without making an assembly unstable. Honours a GC range and excluded motifs (restriction sites) during the search rather than filtering afterwards. Deterministic given a seed: the same inputs give the same toolbox. Returns fewer parts than asked, with a reason, when the constraints leave no room — it never invents a repetitive one to hit the count.
{ "type": "object", "required": [ "constraint" ], "properties": { "lmax": { "type": "integer", "default": 15, "maximum": 40, "minimum": 8, "description": "Longest stretch any two parts may share, in bp (default 15)." }, "seed": { "type": "integer", "default": 1, "description": "Seeds the search. Change it for a different toolbox from the same constraints; keep it to reproduce one." }, "count": { "type": "integer", "default": 20, "maximum": 500, "minimum": 1, "description": "How many parts to build (max 500)." }, "gcMax": { "type": "number", "default": 100, "maximum": 100, "minimum": 0, "description": "Highest GC% a part may have." }, "gcMin": { "type": "number", "default": 0, "maximum": 100, "minimum": 0, "description": "Lowest GC% a part may have." }, "exclude": { "type": "array", "items": { "type": "string" }, "description": "Motifs no part may contain, checked on both strands: restriction sites you clone with, a terminator you do not want. Literal ACGT only — an IUPAC code is refused rather than silently half-matched." }, "background": { "type": "array", "items": { "type": "string" }, "description": "Sequences the new parts must also avoid sharing with — the host genome region, the vector, or a toolbox you already own." }, "constraint": { "type": "string", "description": "The IUPAC template every part must match, e.g. \"NNNNNNTTGACANNNNNNNNNNNNNNNNNTATAATNNNNNN\" for a sigma-70 promoter library. N is any base; fixed letters are held. Max 1,000 nt." }, "bothStrands": { "type": "boolean", "default": true, "description": "Treat a stretch and its reverse complement as the same stretch." } }, "additionalProperties": false }arguments 65 linesoperon_scan unknown never probed
Scan a multi-gene construct, on both strands, for the sequence that quietly breaks operons: promoter-like -35/-10 pairs (including ones pointing backwards, which make antisense RNA), Shine-Dalgarno sequences positioned in front of an internal start codon, terminator-shaped hairpins with a U-tract, out-of-frame start codons inside a declared CDS, and exact direct repeats. Reports what MATCHED and how far it sits from consensus — it does not score a match or claim it transcribes. For an estimated promoter strength use promoter_predict; for a translation rate use rbs_predict.
{ "type": "object", "required": [ "sequence" ], "properties": { "cdsEnd": { "type": "integer", "description": "1-based end of that coding sequence." }, "cdsStart": { "type": "integer", "description": "1-based start of a coding sequence. Given with cdsEnd, out-of-frame start codons inside it are reported — without them that check is skipped, because 'out of frame' has no meaning until a frame is declared." }, "sequence": { "type": "string", "residues": "nt", "description": "The construct, raw, FASTA or GenBank. Max 100,000 bp." }, "maxPromoterMismatches": { "type": "integer", "default": 1, "maximum": 4, "minimum": 0, "description": "Total mismatches allowed across both consensus boxes (default 1). 0 finds only perfect consensus, which real promoters rarely are; above 2 the hit rate on random DNA climbs fast." } }, "additionalProperties": false }arguments 29 linesprimer_site_accessibility unknown never probed
Fold the template around each place a primer binds, at the annealing temperature and under DNA parameters, and report how much of the primer's own footprint sits inside a helix. Primer design tools score the oligo — its Tm, its hairpin, its dimers — and leave the template unexamined, while a binding site buried in a stable stem is an ordinary reason a well-designed primer does not amplify. Returns the folded window, its free energy, the paired fraction of the footprint, and how many of the 3'-terminal five bases are paired.
{ "type": "object", "required": [ "template", "primer" ], "properties": { "primer": { "type": "string", "description": "The primer, 5'->3'." }, "circular": { "type": "boolean", "default": false, "description": "Wrap the window across the origin instead of clipping it." }, "template": { "type": "string", "description": "The template the primer has to bind — the region of interest, a plasmid, or an amplicon." }, "windowNt": { "type": "number", "default": 120, "maximum": 200, "minimum": 40, "description": "Template to fold around each site, centred on the footprint. 40-200 nt." }, "annealingTemp": { "type": "number", "default": 60, "maximum": 95, "minimum": 20, "description": "The annealing temperature in Celsius. This is the whole reason the tool exists — structure at 37 C is not structure at 60 C, and the number changes the answer." }, "maxMismatches": { "type": "number", "maximum": 10, "minimum": 0, "description": "Mismatches allowed when locating the primer. Defaults to the binding scanner's own rate." } }, "additionalProperties": false }arguments 43 linesoperon_design unknown never probed
Build a polycistronic operon from a promoter, a list of CDSs with their RBSs, spacers and a terminator — optionally recoding every CDS for a host — then scan the ASSEMBLED molecule for internal promoters, Shine-Dalgarno sequences, terminators, out-of-frame start codons and repeats. Scanning the product rather than the parts is the point: these elements are very often created BY THE JOIN between two parts, so checking each part alone finds nothing. Returns the sequence, an annotated GenBank file, and every element found. Assigns no translation rate — use rbs_library_design to choose RBSs, then rbs_predict to rank the result.
{ "type": "object", "required": [ "genes" ], "properties": { "name": { "type": "string", "description": "LOCUS name for the GenBank output." }, "genes": { "type": "array", "items": { "type": "object", "required": [ "cds" ], "properties": { "cds": { "type": "string", "description": "The coding sequence, as DNA." }, "rbs": { "type": "string", "description": "Ribosome binding site placed in front of this gene. Omit for a consensus default, or pass \"\" for none." }, "name": { "type": "string", "description": "Label for the CDS feature." } } }, "description": "The genes, in order (max 12)." }, "spacer": { "type": "string", "description": "Sequence inserted between one CDS and the next gene's RBS." }, "promoter": { "type": "string", "description": "Promoter placed at the 5' end." }, "terminator": { "type": "string", "description": "Terminator placed at the 3' end." }, "optimiseFor": { "enum": [ "ecoli", "human", "yeast", "cho", "pichia", "insect", "arabidopsis", "zebrafish" ], "type": "string", "description": "Recode every CDS with this host's most-frequent codons. The rewrite is checked to translate back to the same protein, and skipped for that gene if it does not. This is a determinate recoding, NOT a yield prediction — published codon-optimisation algorithms are close to a coin flip on whether they raise or lower real expression." }, "includeGenbank": { "type": "boolean", "default": true, "description": "Return the annotated GenBank file." } }, "additionalProperties": false }arguments 68 linessynthesis_complexity unknown never probed
Measure the sequence features gene-synthesis vendors screen on — repeats (the single largest cause of synthesis failure), GC extremes, GC swings between adjacent windows, homopolymer runs and hairpin-forming inverted repeats — and report each against the threshold vendors publish. Returns measurements and named flags, never a success probability: refitted on the 303 REAL orders its authors publish (scripts/ssc-eval), the published classifier scores F1 0.866 against 0.878 for assuming every order succeeds, and transfers between ordering labs at AUC 0.423 — below chance. Pair with nonrepetitive_parts_design to fix the repeats it finds.
{ "type": "object", "required": [ "sequence" ], "properties": { "window": { "type": "integer", "default": 50, "maximum": 500, "minimum": 20, "description": "Window for the GC profile, in bp (default 50). Vendors screen local GC, not just the average, so this is what the flags are computed over." }, "sequence": { "type": "string", "residues": "nt", "description": "The fragment as it would be ordered, raw, FASTA or GenBank. Max 100,000 bp." }, "repeatMin": { "type": "integer", "default": 20, "minimum": 8, "description": "Shortest repeated stretch to report, in bp (default 20, which is where vendor repeat filters sit)." }, "includeProfile": { "type": "boolean", "default": false, "description": "Return the full per-window GC profile. Off by default — it is one row per window and most callers want the flags." } }, "additionalProperties": false }arguments 32 linestrace_secondary_peaks unknown never probed
Read a chromatogram for what the basecaller did not report: positions where a second dye is present under the called base (a heterozygote, or a contaminating template), and bases still visible in the scan past where base calling stopped. Both are arithmetic on the channel intensities already in the file — a ratio, and a peak position extrapolated from the median spacing — not a model. Returns the called sequence rewritten with IUPAC ambiguity codes, the extra bases, and every threshold that produced the answer. Takes the SCAN arrays, because the tail lies past the last peak location.
{ "type": "object", "required": [ "baseCalls", "peakLocations", "channelA", "channelC", "channelG", "channelT" ], "properties": { "quality": { "type": "array", "items": { "type": "number" }, "description": "Optional per-base Phred scores; echoed beside each mixed position." }, "channelA": { "type": "array", "items": { "type": "number" }, "description": "Full A channel, indexed by SCAN (not by base)." }, "channelC": { "type": "array", "items": { "type": "number" }, "description": "Full C channel, indexed by scan." }, "channelG": { "type": "array", "items": { "type": "number" }, "description": "Full G channel, indexed by scan." }, "channelT": { "type": "array", "items": { "type": "number" }, "description": "Full T channel, indexed by scan." }, "baseCalls": { "type": "string", "description": "Base calls, e.g. from parse_sanger_trace." }, "mixedRatio": { "type": "number", "default": 0.25, "description": "Secondary/primary intensity ratio at which a position is reported as mixed (0-1 exclusive). A convention, not a measurement." }, "skipLeading": { "type": "number", "default": 40, "description": "Bases at the read's start excluded from the mixed scan (0-1000). The dye blob lives here and lifts every channel; without this every read reports a wall of false heterozygotes at its start." }, "maxExtension": { "type": "number", "default": 400, "description": "Most extra bases to call past the last called base (0-400). The cap is part of the method: peak positions are extrapolated and the extrapolation drifts." }, "peakLocations": { "type": "array", "items": { "type": "number" }, "description": "Scan index of each called base's peak — one per base call." }, "tailSignalToNoise": { "type": "number", "default": 3, "description": "How far above the measured noise floor a channel must sit before the tail extension calls it (1-100)." } }, "additionalProperties": false }arguments 80 linestrace_diagnose unknown never probed
Diagnose a failing Sanger chromatogram: the longest usable window (Mott trimming), whether there is signal above the noise at all, whether more than one molecule is in the tube and from which base, whether quality collapsed at a homopolymer or tandem repeat the polymerase stuttered through, and whether a dye blob or the instrument's own separation is the problem rather than the DNA. Each finding carries the measurement it is based on, what that pattern is usually caused by, and what to do next. Reads .ab1, .abi and .scf.
{ "type": "object", "required": [ "fileBase64" ], "properties": { "fileName": { "type": "string", "description": "Optional original file name (echoed back, and used to explain a refusal)." }, "fileBase64": { "type": "string", "description": "The binary trace file (.ab1 / .abi / .scf), base64-encoded." }, "mixedRatio": { "type": "number", "default": 0.35, "maximum": 0.9, "minimum": 0.1, "description": "A second peak at or above this fraction of the called peak counts as a mixed position. Lower it to catch a minor species, raise it if ordinary crosstalk on your instrument is firing it." }, "qualityCutoff": { "type": "number", "default": 20, "maximum": 60, "minimum": 5, "description": "Phred score the usable window is measured at. 20 is the conventional 1-in-100 line." } }, "additionalProperties": false }arguments 31 linespromoter_library_design unknown never probed
Build a set of sigma-70 promoters that (a) share no more than a chosen length of sequence with each other, so the library does not recombine with itself once integrated, and (b) span a range of predicted transcription rates, picked as an evenly log-spaced ladder. Variants are constructed deterministically from an IUPAC template holding the -35 and -10 consensus; their strengths are then estimated by the Promoter Calculator model. Rungs with no variant near them are reported as gaps rather than filled with the nearest thing. PREDICTED, NOT MEASURED: strengths carry R^2 = 0.45-0.60 against independent in vivo data, so treat the ladder as a ranked set to screen, not as calibrated numbers. PREDICTED, NOT MEASURED. R^2 = 0.45 and 0.60 against the two INDEPENDENT in vivo datasets the authors tested (Hossain et al., 4,350 promoters, Spearman rho = 0.69; Urtecho et al., 10,898 promoters, rho = 0.67). The widely quoted R^2 = 0.80 is a held-out tenth of the authors' OWN in vitro transcription data and is not the number to plan against: a promoter in a cell is the in vivo case, where between a third and a half of the variance is unexplained. Valid for: sigma-70 (housekeeping) promoters in E. coli. NOT valid for another sigma factor, another organism, a promoter under activator or repressor control, or anything about mRNA stability or translation — rbs_predict is the translation half, and neither speaks to the other.
{ "type": "object", "required": [ "librarySize" ], "properties": { "lmax": { "type": "integer", "default": 12, "maximum": 40, "minimum": 8, "description": "Longest stretch any two promoters in the library may share, in bp (default 12). This is the property that stops the library recombining with itself." }, "seed": { "type": "integer", "default": 1, "description": "Seeds variant construction; same seed, same variants." }, "gcMax": { "type": "number", "default": 100, "maximum": 100, "minimum": 0, "description": "Highest GC% a variant may have." }, "gcMin": { "type": "number", "default": 0, "maximum": 100, "minimum": 0, "description": "Lowest GC% a variant may have." }, "exclude": { "type": "array", "items": { "type": "string" }, "description": "Motifs no variant may contain, both strands — the restriction sites you clone with. Literal ACGT only." }, "template": { "type": "string", "description": "IUPAC template every variant must match. Defaults to a sigma-70 layout holding TTGACA and TATAAT with a 17 nt spacer and randomised flanks. Change it to target a different architecture — but a template that randomises the boxes will produce members that are not promoters." }, "targetMax": { "type": "number", "description": "Strongest rung, same units. Omit with targetMin to use the variants' own range." }, "targetMin": { "type": "number", "description": "Weakest rung, in the model's arbitrary transcription-rate units. OMIT THIS and the range is taken from what the built variants actually score, which is usually right: the units have no absolute meaning, so a default would describe nothing. Set it only to match a promoter you measured yourself." }, "librarySize": { "type": "integer", "maximum": 24, "minimum": 2, "description": "How many promoters the ladder should have (2 to 24). Required: every other argument has a defensible default, so this is the one statement of intent, and without it an empty call would build and score a library nobody asked for." }, "candidatePool": { "type": "integer", "default": 24, "maximum": 48, "minimum": 4, "description": "How many variants to build and score before selecting the ladder. A larger pool fills more rungs and costs one longer scan, not more round trips." } }, "additionalProperties": false }arguments 67 linescloning_next_observation unknown never probed
Rank every observation you have not yet made by how many open causes it settles WHICHEVER WAY IT COMES OUT, then return the smallest set of observations that settles all of them. Takes the same arguments as cloning_diagnose. The ranking is computed by re-running the diagnosis at each possible outcome of each observation and intersecting, so every count is a worst case rather than an average — and causes that no observation can settle are named, because those need a different experiment rather than more observing. No probabilities anywhere.
{ "type": "object", "required": [ "symptom", "method" ], "properties": { "parts": { "type": "array", "items": { "type": "string" }, "maxItems": 8, "description": "Parts in assembly order (Golden Gate / Gibson), or [vector, insert] for a restriction ligation. Raw or FASTA. Up to 8; 300,000 bp total across parts and template." }, "method": { "enum": [ "goldengate", "gibson", "restriction_ligation", "pcr" ], "type": "string", "description": "How the construct was made. Decides which cause set applies and which design checks can run." }, "enzymes": { "type": "array", "items": { "type": "string" }, "maxItems": 4, "description": "The Type IIS enzyme for Golden Gate (BsaI, BbsI, Esp3I (BsmBI)), or the one or two restriction enzymes the insert and vector were cut with. An unrecognized name is rejected rather than skipped: every methylation and site-geometry verdict here reads \"no site found\" when the enzyme is missing, so a typo would come back as a clean bill of health." }, "symptom": { "enum": [ "no_colonies", "wrong_clones", "no_pcr_band" ], "type": "string", "description": "The complaint. \"no_colonies\" = the plate is blank; \"wrong_clones\" = colonies grew but the clones are empty vector / rearranged / the original template; \"no_pcr_band\" = the gel lane is empty or the band is the wrong size." }, "colonies": { "type": "number", "description": "Colonies on the experimental plate. Omitting this is different from giving 0." }, "screened": { "type": "object", "required": [ "total", "correct" ], "properties": { "total": { "type": "number", "description": "Clones screened." }, "correct": { "type": "number", "description": "Clones that were the intended construct." }, "rearranged": { "type": "number", "description": "Clones that were a real plasmid but not the intended arrangement of parts." }, "emptyVector": { "type": "number", "description": "Clones carrying no insert." }, "originalTemplate": { "type": "number", "description": "Clones that turned out to be the plasmid the insert was amplified from." } }, "description": "Screening tally, up to 100,000 clones. The buckets must not add up to more than total — an inconsistent tally is rejected rather than reasoned over, because every verdict drawn from the screen compares a count against that total." }, "template": { "type": "string", "residues": "nt", "description": "PCR template, raw or FASTA." }, "ladderRan": { "type": "boolean", "description": "Was the ladder itself visible in the same gel? A true here eliminates the whole stain-and-imaging branch in one observation." }, "partNames": { "type": "array", "items": { "type": "string" }, "description": "Labels for the parts, in the same order (\"backbone\", \"promoter\", \"CDS\"). Used in every fact that names a part." }, "overlapLen": { "type": "number", "default": 20, "description": "Gibson only — the homology arm length the assembly was designed with." }, "insertSource": { "enum": [ "plasmid_pcr", "genomic_pcr", "synthesis", "digest", "unknown" ], "type": "string", "description": "Where the insert came from. Only \"plasmid_pcr\" changes a verdict: a plasmid template replicates and selects on its own, so it can give colonies with no ligation at all." }, "vectorMarker": { "enum": [ "amp", "ampicillin", "bla", "cam", "carb", "carbenicillin", "chlor", "chloramphenicol", "gent", "gentamicin", "hyg", "hygromycin", "kan", "kanamycin", "neo", "spec", "spectinomycin", "strep", "tet", "tetracycline", "zeo", "zeocin" ], "type": "string", "description": "Selection marker on the vector. Compared against the plate's antibiotic by identity, not by guessing at free text." }, "primerForward": { "type": "string", "residues": "nt", "description": "Forward primer, up to 200 nt." }, "primerReverse": { "type": "string", "residues": "nt", "description": "Reverse primer, up to 200 nt." }, "agarosePercent": { "type": "number", "default": 1, "description": "Agarose percentage of the gel. Snapped to the nearest tabulated value; decides the resolving window a band is placed against." }, "annealingTempC": { "type": "number", "description": "Annealing temperature actually used, °C. Compared against each primer's own nearest-neighbor Tm." }, "hostMethylation": { "enum": [ "dam_dcm_plus", "dam_dcm_minus", "unknown" ], "type": "string", "default": "unknown", "description": "Dam/Dcm state of the DNA that was CUT — a property of the strain the plasmid was prepared from, not the one it was transformed into. Standard cloning strains are dam+/dcm+. \"dam_dcm_minus\" eliminates every methylation-blocking cause; \"unknown\" leaves the sequence overlap stated as a fact and the methylation as an open question." }, "plateAntibiotic": { "enum": [ "amp", "ampicillin", "bla", "cam", "carb", "carbenicillin", "chlor", "chloramphenicol", "gent", "gentamicin", "hyg", "hygromycin", "kan", "kanamycin", "neo", "spec", "spectinomycin", "strep", "tet", "tetracycline", "zeo", "zeocin" ], "type": "string", "description": "Antibiotic on the plate. amp and carbenicillin count as the same selection (both select bla)." }, "templateCircular": { "type": "boolean", "default": false, "description": "Treat the template as a plasmid, so a product across the origin is found." }, "gelBandsObservedBp": { "type": "array", "items": { "type": "number" }, "maxItems": 30, "description": "Band sizes read off the lane, bp. An empty array (\"I looked and there was nothing\") is not the same as omitting the field." }, "phosphataseTreated": { "type": "boolean", "description": "Was the cut vector dephosphorylated (rSAP/CIP) before ligation?" }, "noDnaControlColonies": { "type": "number", "description": "Colonies from the same cells and plate with NO DNA added. Non-zero means the plate is not selecting." }, "noInsertControlColonies": { "type": "number", "description": "Colonies from the identical reaction with the insert (or one part) left out." }, "positiveControlColonies": { "type": "number", "description": "Colonies from an intact, uncut plasmid into the same cell aliquot. Non-zero eliminates \"the cells never took up DNA\"." }, "positiveControlSameMarker": { "type": "boolean", "description": "Did that control plasmid carry the SAME selection marker? If not, it eliminates the cells but says nothing about the plate — the tool reports the difference." }, "uncutVectorControlColonies": { "type": "number", "description": "Colonies from the digested but UNLIGATED vector. Measures intact vector that survived the digest, with no help from the ligase." }, "transformationEfficiencyCfuPerUg": { "type": "number", "description": "cfu/µg from a control transformation, where it was measured." } }, "additionalProperties": false }arguments 237 linesread_placement_plan unknown never probed
Given the molecules a cloning reaction could have produced and the sequencing primers you could use, work out which primers separate which pairs of candidates — and return the smallest set that separates every pair any of them can. Scores a read by discrimination, not coverage: a read of 700 bases every candidate shares is worth nothing, and a short read across a junction is worth everything. Names the pairs no primer here separates, so you find out before paying for the reads rather than after. Pair it with outcome_deconvolve once the traces come back.
{ "type": "object", "required": [ "candidates", "primers" ], "properties": { "primers": { "type": "array", "items": { "type": "object" }, "description": "Sequencing primers to choose between, as { id, label, sequence }. Up to 32." }, "candidates": { "type": "array", "items": { "type": "object" }, "description": "The molecules this reaction could produce, as { id, label, sequence, circular? }. Between 2 and 24; assembly_outcomes' intended plus alternatives is the intended source." }, "usableFrom": { "type": "number", "default": 30, "description": "Bases after the primer's 3' end before the trace becomes readable (0-500). A difference inside this dead zone is not counted as a separation, because the trace cannot show it." }, "usableLength": { "type": "number", "default": 700, "description": "Readable bases per reaction, counted from usableFrom (50-5000)." }, "maxMismatches": { "type": "number", "description": "Mismatch budget passed to the priming scan. Defaults to primer-binding's own (~10% of the primer's length)." } }, "additionalProperties": false }arguments 38 linesbase_edit_quant unknown never probed
Quantify CBE/ABE base editing from a pair of Sanger traces — an unedited control and the edited pool — without NGS. At each editable position in the activity window the edited trace is treated as a mixture of the unedited and converted peaks, and the control's OWN alt-channel signal at that same position is subtracted as background, because dye crosstalk is position- and context-dependent and a global constant would be wrong per position. Significance comes from a null built from the same sample (every control position outside the window carrying the same base), so the threshold adapts to the run's chemistry instead of being hardcoded. Returns per-position percentages with z-scores, the target and its bystanders, the background distribution (including a robust estimate of its spread and a count of its outliers), and the noise floor — the percentage the background alone reaches, or null when the run's own null has no spread to derive one from. A window position whose control already carries the converted base is reported but not quantified, because the (1 − b) rescale amplifies error by 1/(1 − b) and turns a 0.1-point wobble into half the pool. Locate the window with an editor id plus the protospacer, or give it explicitly. Blind to indels, which shift the trace rather than mixing a base. PREDICTED, NOT MEASURED. None is published for this implementation. Every run instead reports what it rests on: the background mean, sd, robust (MAD-based) sd, outlier count and n, and a noiseFloorPercent that says how much apparent editing the background alone reaches at the significance threshold — null, rather than 0, when the run has no null with any spread to derive a limit from. This implementation's recovery of known synthetic mixtures (to under a percentage point) is deliberately NOT offered as validation — it tests the arithmetic and the coordinate handling, not whether the linear mixture model fits a real capillary trace. Two properties ARE characterized. The bias is directional and one-sided: the (1 − b) rescale assumes a fully converted position would read as alt fraction 1.0, which real chemistry does not reach, so percentages run low by roughly the crosstalk fraction (order 5-10% relative at typical 3% bleed). The variance is not constant across positions: dividing by (1 − b) amplifies the error in a and b by 1/(1 − b), so the variance of the estimate goes as 1/(1 − b)². Positions whose control alt fraction b exceeds 0.25 are therefore reported but NOT quantified, which bounds that amplification at 1.33x on everything the tool does quantify. Valid for: A pool edited by a cytosine or adenine base editor, read on the same amplicon and chemistry as an unedited control that starts within ±40 bases of it, where the editing is a SUBSTITUTION. Not valid for indels — a base editor also makes them, and an indel-bearing allele shifts the downstream trace so that it degrades the fit at every window position rather than showing up anywhere. Not valid where the control read already carries the alt base at a window position (a pre-existing variant, or the wrong control), since then there is nothing left to correct against — that condition is DETECTED rather than only described: a window position whose control alt fraction exceeds 0.25 is reported with an excludedReason and an editedPercent of 0 instead of a number, warned about, and failed by the hard control-supports-the-window-base-calls gate check. Reported percentages are pool-level: Sanger sees the superposition, so which allele carries which combination of bystander edits is not recoverable from it at all.
{ "type": "object", "required": [ "controlBases", "controlChannels", "editedBases", "editedChannels" ], "properties": { "to": { "type": "string", "residues": "nt", "description": "Explicit-window mode: the base it converts to, as READ on the control strand." }, "from": { "type": "string", "residues": "nt", "description": "Explicit-window mode: the base the editor converts, as READ on the control strand (C for a CBE read forward, G for one read reverse)." }, "editor": { "enum": [ "be3", "be4max", "abe7.10", "abe8e" ], "type": "string", "description": "Base editor id (be3, be4max, abe7.10, abe8e) — fixes the converted bases and the activity window in protospacer coordinates. Requires \"protospacer\". Mutually exclusive with the explicit window arguments." }, "offset": { "type": "number", "description": "Override the alignment offset between the reads (edited position p matches control position p + offset). Whole numbers only. By default it is found from the base calls outside the window; either way the identity reported back is the identity AT THE OFFSET USED, so overriding it does not hide a bad alignment behind the best-scoring one." }, "windowEnd": { "type": "number", "description": "Explicit window end, 1-based inclusive, in CONTROL coordinates. Window length is capped at 40." }, "zThreshold": { "type": "number", "default": 3, "maximum": 10, "minimum": 1, "description": "Significance threshold in standard deviations of the sample's own background. Must be between 1 and 10 — a value outside that range is REJECTED, not clamped, because a run silently retested at a threshold the caller did not choose looks exactly like one that was. Raising it raises the reported noise floor with it." }, "editedBases": { "type": "string", "residues": "nt", "description": "Base calls of the edited pool's read." }, "protospacer": { "type": "string", "residues": "nt", "description": "The 20-nt spacer, located in the CONTROL read. Found on either strand; a reverse-complement match numbers the protospacer right-to-left along the read and complements the converted bases (a CBE's C→T reads as G→A), which is handled. Must match exactly once." }, "windowStart": { "type": "number", "description": "Explicit window start, 1-based in CONTROL read coordinates. Requires windowEnd, from and to." }, "controlBases": { "type": "string", "residues": "nt", "description": "Base calls of the UNEDITED control read." }, "editedChannels": { "type": "array", "items": { "type": "array", "items": { "type": "number" } }, "description": "Per-base [A, C, G, T] intensities of the edited read, same convention." }, "targetPosition": { "type": "number", "description": "1-based CONTROL position of the intended edit. Give it when you know it: without it the most-edited significant position is labeled the target and the rest become bystanders, which relabels a bystander-dominant result as a clean one." }, "controlChannels": { "type": "array", "items": { "type": "array", "items": { "type": "number" } }, "description": "Per-base [A, C, G, T] intensities of the control read, one row per called base, read at that base's peak location (trace arrays are indexed by scan, not by base)." }, "targetProtospacerPosition": { "type": "number", "description": "1-based protospacer position of the intended edit (PAM-distal = 1). Editor mode only." } }, "additionalProperties": false }arguments 94 linesvariant_comparator unknown never probed
Align a query to a reference and call variants (substitutions, insertions, deletions) in HGVS g. notation, with optional coding effects.
{ "type": "object", "required": [ "reference", "query" ], "properties": { "query": { "type": "string", "residues": "nt", "description": "Query / variant sequence (raw or FASTA)." }, "coding": { "type": "boolean", "default": false, "description": "Treat as a coding sequence and report amino-acid effects." }, "reference": { "type": "string", "residues": "nt", "description": "Reference / wild-type sequence (raw or FASTA)." }, "frameStart": { "type": "integer", "default": 1, "description": "1-based reading-frame start (used when coding is true)." } }, "additionalProperties": false }arguments 30 linessanger_knockin_quant unknown never probed
Measure the rate of a SPECIFIC intended edit from a pair of Sanger traces — an unedited control and the edited pool — by decomposing the edited trace onto three things at once: the wild-type allele, the intended edited allele, and the unintended indels. Serves both readouts that need this: HDR knock-in rate (what fraction of the pool carries the donor's edit, including an insert of novel sequence), and prime editing (the pegRNA's intended substitution, insertion, deletion or replacement as the intended column, and the indel byproducts at the nick as the shift columns). This is what sanger_indel_spectrum cannot do: that tool's basis is indexed by indel LENGTH, so an intended 6 bp knock-in and an accidental 6 bp NHEJ deletion are one column there. Returns knock-in / wild-type / unintended-indel percentages, the byproduct spectrum by shift, and the R² that says whether the model fits your traces at all. Non-negative least squares, so no allele is ever assigned a negative share. For a substitution or replacement the reference allele you name is checked against the control read before anything is fitted; an insertion and a deletion name no reference bases, so there only the position can be range-checked. PREDICTED, NOT MEASURED. Every run reports its own R²: how much of the observed window the basis actually explains, measured on YOUR traces, where a low value means the model is wrong here rather than that the edit is weak. On agreement with a reference method for real samples — amplicon sequencing or clonal genotyping — none is published for this implementation. The underlying decomposition is TIDE/TIDER's, whose authors report their own concordance, and that number does not transfer to this code so it is not quoted. This implementation's near-exact recovery of synthetic mixtures is deliberately not offered as validation: a synthetic mixture is built from the same idealised one-hot peaks the basis assumes, so recovering it tests the arithmetic and cannot test the assumption. Valid for: A pool whose intended edit is known EXACTLY, read against a control amplicon of the same locus and chemistry, with both reads extending well past the edit. The novel inserted bases of a knock-in carry an assumed peak shape rather than a measured one (returned as constructedPositions) — the more of the window they occupy, the more of the fit is testing that assumption. NOT valid when the reported R² is low; nor for separating an intended pure DELETION from an unintended indel of the same net length ANYWHERE in the window, not only one at the same site (the tool reports which case it is in `sameShiftByproduct`: when that column is not fitted, knockinPercent is the sum of the two); nor for telling an on-target knock-in from a random integration of the same donor; nor for resolving haplotypes, since a Sanger trace of a pool has no phase information.
{ "type": "object", "required": [ "controlBases", "controlChannels", "editedBases", "editedChannels", "editKind", "editPosition" ], "properties": { "offset": { "type": "number", "description": "Override the alignment offset between the reads (whole number, −40 to 40). By default it is found from the base calls upstream of the edit. upstreamIdentity is always measured AT the offset used, so an override that is wrong shows up as a failed same-amplicon check rather than borrowing the auto-detected offset's score." }, "editKind": { "enum": [ "substitution", "insertion", "deletion", "replacement" ], "type": "string", "description": "Shape of the intended edit, spelled as prime_editing_design spells it. \"substitution\" replaces bases one for one; \"insertion\" adds novel bases and replaces none; \"deletion\" removes bases and adds none; \"replacement\" is the general case where the two lengths differ." }, "maxIndel": { "type": "number", "default": 10, "description": "Largest unintended indel to fit, in bp (1-20; out of range is rejected, not clamped). Every shift from −maxIndel to +maxIndel is included except 0, which is wild-type. The intended edit's OWN net shift is included too whenever its column is measurably different from the intended-edit column — it is dropped only when the two are the same vector, which happens for a pure deletion whose cut is at the edit. See sameShiftByproduct in the result for which of the two happened." }, "altAllele": { "type": "string", "residues": "nt", "description": "The bases the edit installs in their place (substitution and replacement)." }, "refAllele": { "type": "string", "residues": "nt", "description": "The control bases the edit replaces (substitution and replacement). Checked against the control read: a mismatch is rejected, because building the intended-edit column at the wrong position yields a confident, meaningless number." }, "cutPosition": { "type": "number", "description": "1-based CONTROL position where UNINTENDED indels start — the nuclease cut or the PE nick. Defaults to the edit start. Separate from editPosition because a byproduct allele is wild-type up to the cut and shifted after it, so a wrong cut position makes those columns wrong over the first part of the window." }, "editedBases": { "type": "string", "residues": "nt", "description": "Base calls of the edited pool's read." }, "insertedSeq": { "type": "string", "residues": "nt", "description": "The novel bases inserted (insertion only)." }, "controlBases": { "type": "string", "residues": "nt", "description": "Base calls of the UNEDITED control read." }, "editPosition": { "type": "number", "description": "1-based position of the edit in CONTROL read coordinates: the first base the edit replaces. An insertion replaces nothing, so there it is the base the insert lands immediately BEFORE — one MORE than the VCF/HGVS anchor, which names the base before an insertion. The rule is uniform across all four kinds on purpose; a spec transcribed from VCF needs +1 on an insertion." }, "windowLength": { "type": "number", "default": 70, "description": "Bases from the edit site downstream used for the decomposition (20-300; out of range is rejected, not clamped). Unlike sanger_indel_spectrum there is no guard region: the edited positions themselves are the only signal separating a substitution from wild-type." }, "deletedLength": { "type": "number", "description": "How many bases are deleted (deletion only)." }, "editedChannels": { "type": "array", "items": { "type": "array", "items": { "type": "number" } }, "description": "Per-base [A, C, G, T] intensities of the edited read, same convention." }, "controlChannels": { "type": "array", "items": { "type": "array", "items": { "type": "number" } }, "description": "Per-base [A, C, G, T] intensities of the control read, one row per called base, read at that base's peak location (trace arrays are indexed by scan, not by base)." } }, "additionalProperties": false }arguments 95 linesediting_plate_quantify unknown never probed
Quantify a whole plate of edited samples against ONE untreated control trace and return a single sortable table — the plate-scale form of sanger_indel_spectrum, base_edit_quant and sanger_knockin_quant, chosen with `mode`. Each sample gives one row keyed by its id, carrying the headline number for that mode (edited fraction / editing at the target base / intended knock-in percentage), the fit-quality numbers behind it (R², or the background n and noise floor for base mode), and fitAdequate — the single-sample tool's own gate verdict on that row, so the plate cannot drift from the per-well answer. Failure is isolated per well: a sample whose read is short, mismatched or unfittable becomes a failed ROW with its error message and the other 95 still come back, while an error about the control trace, the mode or the work ceilings throws, because it is wrong for every row. Duplicate sample ids are suffixed (against the whole plate, so the suffix never lands on another well's name) rather than merged. Arguments are strict: an argument belonging to another mode, an unknown argument, an out-of-range limit, and an `offset` override (which is a property of one pair of reads, not of a plate) are all rejected rather than ignored or clamped, because at plate scale a substituted setting rewrites every row identically and nothing in the table looks odd. Returns the rows in input order, a tally, and a CSV. Comparing two wells' percentages is only meaningful when both rows are fitAdequate, which is why the plate summary is computed over those rows alone. PREDICTED, NOT MEASURED. None is published for this implementation, and being a batch does not soften that: each row is exactly the claim the corresponding single-sample tool makes. What every row instead reports is what it rests on — R² for the indel and knock-in modes, the background n, sd and noise floor for base mode — plus fitAdequate, which is the single-sample tool's OWN gate verdict on that row rather than a threshold re-invented here. Recovery of known synthetic mixtures is deliberately NOT offered as validation: it tests the arithmetic and the plate plumbing, not whether the model fits a real capillary trace, and for a knock-in with novel inserted bases it is circular, because a synthetic trace is built from the same idealised peaks the basis assumes. Quoting it would be the mistake rbs_predict made when it shipped a calibration residual as held-out skill. Valid for: One control read and a set of edited reads that are all the SAME amplicon, chemistry and primer as that control, with each read extending well past the edit site. COMPARING TWO WELLS' PERCENTAGES IS ONLY MEANINGFUL WHEN BOTH ROWS ARE fitAdequate: a percentage from a badly fitting well is not a smaller number than one from a well that fitted, it is a different kind of statement, and the plate summary here is therefore computed over the adequate rows only. Ranking wells also assumes they differ only in the variable under test — the same control is subtracted from all of them, so a well whose read started 30 bases later or whose reaction was dirty carries that difference into its number. Mode-specific limits carry over unchanged: indel mode is blind to substitutions, base mode is blind to indels and its percentages run low by roughly the crosstalk fraction, and knock-in mode cannot separate an intended pure deletion from an NHEJ deletion of the same length at the same site.
{ "type": "object", "required": [ "mode", "controlBases", "controlChannels", "samples" ], "properties": { "to": { "type": "string", "residues": "nt", "description": "base mode: the base it converts to, as READ on the control strand." }, "from": { "type": "string", "residues": "nt", "description": "base mode: the base the editor converts, as READ on the control strand." }, "mode": { "enum": [ "indel", "base", "knockin" ], "type": "string", "description": "Which quantifier to run on every well. \"indel\" = sanger_indel_spectrum (NHEJ efficiency and the indel spectrum; needs cutPosition; blind to substitutions). \"base\" = base_edit_quant (CBE/ABE conversion; needs an editor id + protospacer, or an explicit window with from/to; blind to indels). \"knockin\" = sanger_knockin_quant (a specific intended edit against its byproducts; needs editKind + editPosition). Arguments belonging to another mode are rejected, not ignored." }, "guard": { "type": "number", "default": 3, "description": "indel mode: bases skipped immediately after the cut, where the trace is least reliable. A whole number >= 0; a negative value is rejected, not clamped to 0." }, "editor": { "enum": [ "be3", "be4max", "abe7.10", "abe8e" ], "type": "string", "description": "base mode: base editor id (be3, be4max, abe7.10, abe8e) — fixes the converted bases and the activity window in protospacer coordinates. Requires \"protospacer\". Mutually exclusive with windowStart/windowEnd/from/to." }, "samples": { "type": "array", "items": { "type": "object", "required": [ "bases", "channels" ], "properties": { "id": { "type": "string", "description": "Well or sample name — this keys the row. A number is tolerated and read as its digits. Duplicates are suffixed (\"A01#2\", stepping past any name already in use), never merged; an empty or absent id becomes sample_<n>." }, "bases": { "type": "string", "description": "Base calls of this well's read (raw or FASTA)." }, "channels": { "type": "array", "items": { "type": "array", "items": { "type": "number", "minimum": 0 } }, "description": "Per-base [A, C, G, T] intensities for this well, same convention as the control, and non-negative for the same reason." } }, "additionalProperties": false }, "maxItems": 384, "description": "The plate's edited wells, in the order you want them tabulated. Up to 384 samples (96 is the natural plate) and 400,000 trace positions across the whole call, control included — that is already an 8-10 MB request body, so split a plate of untrimmed reads rather than sending one call." }, "editKind": { "enum": [ "substitution", "insertion", "deletion", "replacement" ], "type": "string", "description": "knockin mode (required): shape of the intended edit. \"substitution\" replaces bases one for one; \"insertion\" adds novel bases and replaces none; \"deletion\" removes bases and adds none; \"replacement\" is the general case where the lengths differ." }, "maxIndel": { "type": "number", "default": 10, "description": "indel and knockin modes: largest indel to fit, in bp — a whole number, 1-20. Out of range is rejected, not clamped." }, "altAllele": { "type": "string", "residues": "nt", "description": "knockin mode: the bases installed in their place." }, "refAllele": { "type": "string", "residues": "nt", "description": "knockin mode: the control bases the edit replaces (substitution and replacement). Checked against the control read once, before any well is fitted." }, "windowEnd": { "type": "number", "description": "base mode: explicit window end, 1-based inclusive. Window length is capped at 40." }, "zThreshold": { "type": "number", "default": 3, "description": "base mode: significance threshold in standard deviations of each well's own background (1-10; out of range is rejected, not clamped). Raising it raises the reported noise floor with it." }, "cutPosition": { "type": "number", "description": "indel mode (required): 1-based position of the expected cut, in CONTROL read coordinates. knockin mode (optional): 1-based CONTROL position where UNINTENDED indels start — the nuclease cut or the PE nick; defaults to the edit start." }, "insertedSeq": { "type": "string", "residues": "nt", "description": "knockin mode: the novel bases inserted (insertion only)." }, "protospacer": { "type": "string", "residues": "nt", "description": "base mode: the 20-nt spacer, located in the CONTROL read (either strand; must match exactly once)." }, "windowStart": { "type": "number", "description": "base mode: explicit window start, 1-based in CONTROL coordinates. Requires windowEnd, from and to." }, "controlBases": { "type": "string", "residues": "nt", "description": "Base calls of the ONE untreated control read (raw or FASTA)." }, "editPosition": { "type": "number", "description": "knockin mode (required): 1-based CONTROL position of the first base the edit replaces. An insertion replaces nothing, so there it is the base the insert lands immediately BEFORE — one MORE than the VCF/HGVS anchor." }, "windowLength": { "type": "number", "default": 70, "description": "indel and knockin modes: bases downstream used for the decomposition — a whole number, 20-300. Out of range is rejected, not clamped." }, "deletedLength": { "type": "number", "description": "knockin mode: how many bases are deleted (deletion only)." }, "targetPosition": { "type": "number", "description": "base mode: 1-based CONTROL position of the intended edit. Give it for a plate. Without it each well's headline is its OWN most-edited significant position, so two rows can be reporting two different bases and the column is not one measurement." }, "controlChannels": { "type": "array", "items": { "type": "array", "items": { "type": "number", "minimum": 0 } }, "maxItems": 3000, "description": "Per-base [A, C, G, T] intensities of the control read, one row per called base, read at that base's peak location (trace arrays are indexed by scan, not by base). Raw peak heights: every intensity must be >= 0, because negatives are clamped to zero during normalization and a baseline-subtracted trace would silently lose its minor peaks and read as unedited." }, "targetProtospacerPosition": { "type": "number", "description": "base mode: 1-based protospacer position of the intended edit (PAM-distal = 1). Editor mode only." } }, "additionalProperties": false }arguments 170 linesmultiplex_panel_design unknown never probed
Choose one primer pair per target so the whole panel works in one tube: no cross-dimer between any two of the primers, every amplicon resolvable from every other on the gel you will run, and one annealing temperature that serves all of them. Searches combinations rather than picking each target's best pair in isolation, which is what makes panels fail — and when no compatible panel exists it names the target pairs that cannot be multiplexed at all, so you know which one to redesign.
{ "type": "object", "required": [ "targets" ], "properties": { "targets": { "type": "array", "items": { "type": "object", "required": [ "template" ], "properties": { "label": { "type": "string", "description": "Name for this target, used throughout the result." }, "template": { "type": "string", "description": "Template sequence, raw or FASTA." }, "targetEnd": { "type": "number", "description": "1-based inclusive end of that region." }, "ampliconMax": { "type": "number", "description": "Largest product for this target." }, "ampliconMin": { "type": "number", "description": "Smallest product for THIS target. Giving each target its own size band is how a panel is made readable — leaving them all on one range makes comigration the dominant conflict." }, "targetStart": { "type": "number", "description": "1-based start of the region the product must span." } } }, "description": "2-8 targets to amplify in one reaction." }, "ampliconMax": { "type": "number", "description": "Panel-wide default product size ceiling." }, "ampliconMin": { "type": "number", "description": "Panel-wide default product size floor, for targets that set none." }, "maxTmSpread": { "type": "number", "default": 3, "description": "Widest Tm difference tolerated across every primer in the panel, in °C — one annealing temperature has to serve all of them." }, "agarosePercent": { "type": "number", "description": "Gel the panel will be read on. Omit and the percentage whose resolving window contains the amplicons is chosen and reported — a panel of small products judged on a 1% gel reads as all-comigrating, which is about the gel rather than the primers." }, "dimerThresholdDG": { "type": "number", "default": -6, "description": "ΔG (kcal/mol) at or below which a cross-dimer involving a primer's 3' END is a conflict. That end is where extension starts, so it matters at a weaker ΔG than an internal pairing." }, "candidatesPerTarget": { "type": "number", "default": 4, "description": "Candidate pairs considered per target (max 6). More finds a panel where fewer cannot, at the cost of a larger search." }, "internalDimerThresholdDG": { "type": "number", "default": -9, "description": "The looser bar for a cross-dimer that pairs internally and only sequesters primer." } }, "additionalProperties": false }arguments 77 linescloning_diagnose unknown never probed
Work out why a cloning experiment failed: no colonies, every clone empty vector, or no PCR band. Takes your design (method, parts, enzymes, primers, host methylation state) plus what you actually observed (colony counts on the plate and on each control, screening tally, band sizes, whether the ladder ran) and returns causes ranked by evidence — each with the deterministic fact from the design or the observation that implicates it, the cheapest observation that would separate it from the next candidate, and the next experiment. Causes the observations eliminate are reported as eliminated, naming the observation that did it; causes the design makes impossible are not listed. No probability is computed anywhere — the ordering is of evidence, not of likelihood, and `ranking.evidenceBased` says so when the inputs separate nothing.
{ "type": "object", "required": [ "symptom", "method" ], "properties": { "parts": { "type": "array", "items": { "type": "string" }, "maxItems": 8, "description": "Parts in assembly order (Golden Gate / Gibson), or [vector, insert] for a restriction ligation. Raw or FASTA. Up to 8; 300,000 bp total across parts and template." }, "method": { "enum": [ "goldengate", "gibson", "restriction_ligation", "pcr" ], "type": "string", "description": "How the construct was made. Decides which cause set applies and which design checks can run." }, "enzymes": { "type": "array", "items": { "type": "string" }, "maxItems": 4, "description": "The Type IIS enzyme for Golden Gate (BsaI, BbsI, Esp3I (BsmBI)), or the one or two restriction enzymes the insert and vector were cut with. An unrecognized name is rejected rather than skipped: every methylation and site-geometry verdict here reads \"no site found\" when the enzyme is missing, so a typo would come back as a clean bill of health." }, "symptom": { "enum": [ "no_colonies", "wrong_clones", "no_pcr_band" ], "type": "string", "description": "The complaint. \"no_colonies\" = the plate is blank; \"wrong_clones\" = colonies grew but the clones are empty vector / rearranged / the original template; \"no_pcr_band\" = the gel lane is empty or the band is the wrong size." }, "colonies": { "type": "number", "description": "Colonies on the experimental plate. Omitting this is different from giving 0." }, "screened": { "type": "object", "required": [ "total", "correct" ], "properties": { "total": { "type": "number", "description": "Clones screened." }, "correct": { "type": "number", "description": "Clones that were the intended construct." }, "rearranged": { "type": "number", "description": "Clones that were a real plasmid but not the intended arrangement of parts." }, "emptyVector": { "type": "number", "description": "Clones carrying no insert." }, "originalTemplate": { "type": "number", "description": "Clones that turned out to be the plasmid the insert was amplified from." } }, "description": "Screening tally, up to 100,000 clones. The buckets must not add up to more than total — an inconsistent tally is rejected rather than reasoned over, because every verdict drawn from the screen compares a count against that total." }, "template": { "type": "string", "residues": "nt", "description": "PCR template, raw or FASTA." }, "ladderRan": { "type": "boolean", "description": "Was the ladder itself visible in the same gel? A true here eliminates the whole stain-and-imaging branch in one observation." }, "partNames": { "type": "array", "items": { "type": "string" }, "description": "Labels for the parts, in the same order (\"backbone\", \"promoter\", \"CDS\"). Used in every fact that names a part." }, "overlapLen": { "type": "number", "default": 20, "description": "Gibson only — the homology arm length the assembly was designed with." }, "insertSource": { "enum": [ "plasmid_pcr", "genomic_pcr", "synthesis", "digest", "unknown" ], "type": "string", "description": "Where the insert came from. Only \"plasmid_pcr\" changes a verdict: a plasmid template replicates and selects on its own, so it can give colonies with no ligation at all." }, "vectorMarker": { "enum": [ "amp", "ampicillin", "bla", "cam", "carb", "carbenicillin", "chlor", "chloramphenicol", "gent", "gentamicin", "hyg", "hygromycin", "kan", "kanamycin", "neo", "spec", "spectinomycin", "strep", "tet", "tetracycline", "zeo", "zeocin" ], "type": "string", "description": "Selection marker on the vector. Compared against the plate's antibiotic by identity, not by guessing at free text." }, "primerForward": { "type": "string", "residues": "nt", "description": "Forward primer, up to 200 nt." }, "primerReverse": { "type": "string", "residues": "nt", "description": "Reverse primer, up to 200 nt." }, "agarosePercent": { "type": "number", "default": 1, "description": "Agarose percentage of the gel. Snapped to the nearest tabulated value; decides the resolving window a band is placed against." }, "annealingTempC": { "type": "number", "description": "Annealing temperature actually used, °C. Compared against each primer's own nearest-neighbor Tm." }, "hostMethylation": { "enum": [ "dam_dcm_plus", "dam_dcm_minus", "unknown" ], "type": "string", "default": "unknown", "description": "Dam/Dcm state of the DNA that was CUT — a property of the strain the plasmid was prepared from, not the one it was transformed into. Standard cloning strains are dam+/dcm+. \"dam_dcm_minus\" eliminates every methylation-blocking cause; \"unknown\" leaves the sequence overlap stated as a fact and the methylation as an open question." }, "plateAntibiotic": { "enum": [ "amp", "ampicillin", "bla", "cam", "carb", "carbenicillin", "chlor", "chloramphenicol", "gent", "gentamicin", "hyg", "hygromycin", "kan", "kanamycin", "neo", "spec", "spectinomycin", "strep", "tet", "tetracycline", "zeo", "zeocin" ], "type": "string", "description": "Antibiotic on the plate. amp and carbenicillin count as the same selection (both select bla)." }, "templateCircular": { "type": "boolean", "default": false, "description": "Treat the template as a plasmid, so a product across the origin is found." }, "gelBandsObservedBp": { "type": "array", "items": { "type": "number" }, "maxItems": 30, "description": "Band sizes read off the lane, bp. An empty array (\"I looked and there was nothing\") is not the same as omitting the field." }, "phosphataseTreated": { "type": "boolean", "description": "Was the cut vector dephosphorylated (rSAP/CIP) before ligation?" }, "noDnaControlColonies": { "type": "number", "description": "Colonies from the same cells and plate with NO DNA added. Non-zero means the plate is not selecting." }, "noInsertControlColonies": { "type": "number", "description": "Colonies from the identical reaction with the insert (or one part) left out." }, "positiveControlColonies": { "type": "number", "description": "Colonies from an intact, uncut plasmid into the same cell aliquot. Non-zero eliminates \"the cells never took up DNA\"." }, "positiveControlSameMarker": { "type": "boolean", "description": "Did that control plasmid carry the SAME selection marker? If not, it eliminates the cells but says nothing about the plate — the tool reports the difference." }, "uncutVectorControlColonies": { "type": "number", "description": "Colonies from the digested but UNLIGATED vector. Measures intact vector that survived the digest, with no help from the ligase." }, "transformationEfficiencyCfuPerUg": { "type": "number", "description": "cfu/µg from a control transformation, where it was measured." } }, "additionalProperties": false }arguments 237 linesprotein_properties unknown never probed
Protein properties: molecular weight, isoelectric point, GRAVY, extinction coefficient and composition.
{ "type": "object", "required": [ "sequence" ], "properties": { "sequence": { "type": "string", "residues": "aa", "description": "Protein sequence (one-letter amino-acid codes; non-AA characters ignored)." }, "chargeStep": { "type": "number", "default": 0.25, "maximum": 14, "minimum": 0.001, "description": "pH step along the net-charge titration curve, which always spans pH 0-14. Between 0.001 and 14." } }, "additionalProperties": false }arguments 21 linesprotease_digestion unknown never probed
In-silico protease/chemical digestion: cleave a protein and report each peptide's position, length and neutral mass. CNBr masses assume terminal Met becomes homoserine lactone; the sequence retains M and the response labels the modification.
{ "type": "object", "required": [ "sequence" ], "properties": { "maxMass": { "type": "number", "description": "Optional upper bound on neutral monoisotopic mass (Da)." }, "minMass": { "type": "number", "description": "Optional lower bound on neutral monoisotopic mass (Da)." }, "protease": { "enum": [ "trypsin", "lysc", "argc", "chymotrypsin", "gluc", "aspn", "cnbr" ], "type": "string", "default": "trypsin", "description": "Protease or chemical cleavage agent." }, "sequence": { "type": "string", "residues": "aa", "description": "Protein sequence (one-letter amino-acid codes; non-AA characters ignored)." }, "maxPeptides": { "type": "integer", "default": 2000, "description": "Cap on the number of returned peptides." }, "missedCleavages": { "enum": [ 0, 1, 2 ], "type": "integer", "default": 0, "description": "Allowed missed internal cleavages (0–2)." } }, "additionalProperties": false }arguments 51 linescodon_optimize unknown never probed
Codon-optimize a protein (or coding DNA) for an expression host by picking the most-frequent codon per residue.
{ "type": "object", "required": [ "protein" ], "properties": { "protein": { "type": "string", "residues": "any", "description": "Protein sequence (one-letter codes). Coding DNA/RNA is accepted and translated in frame +1 up to the first stop codon (residues after an in-frame stop are NOT optimized)." }, "organism": { "enum": [ "ecoli", "human", "yeast", "cho", "pichia", "insect", "arabidopsis", "zebrafish" ], "type": "string", "default": "ecoli" }, "inputType": { "enum": [ "auto", "protein", "dna" ], "type": "string", "default": "auto", "description": "How to read `protein`. 'auto' guesses from the alphabet (>90% ACGTUN reads as DNA), which mis-files genuine Ala/Cys/Gly/Thr/Asn-only peptides — set 'protein' or 'dna' to force it." } }, "additionalProperties": false }arguments 38 linescodon_adaptation_index unknown never probed
Codon Adaptation Index (CAI) and per-codon relative adaptiveness of a CDS against an expression host, with rare-codon and GC3 analysis.
{ "type": "object", "required": [ "sequence" ], "properties": { "organism": { "enum": [ "ecoli", "human", "yeast", "cho", "pichia", "insect", "arabidopsis", "zebrafish" ], "type": "string", "default": "ecoli" }, "sequence": { "type": "string", "residues": "nt", "description": "Coding sequence (DNA/RNA; should start in-frame at ATG)." }, "frameStart": { "type": "integer", "default": 1, "description": "1-based position to start reading codons." }, "minRareRun": { "type": "integer", "default": 3, "description": "Shortest stretch of CONSECUTIVE rare codons to report as a run. A CAI is a geometric mean, so fifteen rare codons scattered singly and the same fifteen in three runs of five score alike and carry the same rareCount; only the runs say where they are clustered." }, "rareThreshold": { "type": "number", "default": 0.1, "description": "Relative adaptiveness (w) below this flags a codon as rare." } }, "additionalProperties": false }arguments 43 linespairwise_alignment unknown never probed
Global (Needleman-Wunsch), local (Smith-Waterman) or semi-global/fitting pairwise alignment of two sequences, with match/mismatch scoring and affine gap costs (Gotoh).
{ "type": "object", "required": [ "seqA", "seqB" ], "properties": { "gap": { "type": "number", "default": -2, "description": "Affine gap EXTEND penalty, charged per gap position (including the first)." }, "mode": { "enum": [ "global", "local", "semiglobal" ], "type": "string", "default": "global", "description": "\"global\" penalizes end gaps in both sequences; \"local\" returns the best-scoring subalignment; \"semiglobal\" is a fitting alignment — seqB is consumed end to end while seqA's terminal overhangs are free and are not emitted, so a partial read placed on a longer reference is not smeared across it." }, "seqA": { "type": "string", "residues": "any", "description": "First sequence (raw or FASTA; nucleotide or protein)." }, "seqB": { "type": "string", "residues": "any", "description": "Second sequence (raw or FASTA; nucleotide or protein)." }, "match": { "type": "number", "default": 1, "description": "Match score." }, "gapOpen": { "type": "number", "description": "Extra one-off penalty charged on top of gap for a gap's first position. Defaults to 1.5 * gap, so a k-base gap costs gap * (k + 1.5) and one contiguous k-base indel is cheaper than k scattered 1-base gaps. Pass 0 for a purely linear penalty." }, "mismatch": { "type": "number", "default": -1, "description": "Mismatch penalty." } }, "additionalProperties": false }arguments 49 linesmultiple_sequence_alignment unknown never probed
Center-star multiple sequence alignment of a multi-FASTA input — nucleotide or protein, detected from the records and reported as `type` — with consensus and per-column conservation.
{ "type": "object", "required": [ "input" ], "properties": { "input": { "type": "string", "residues": "any", "description": "Two or more sequences in multi-FASTA format (>name / sequence), nucleotide or protein. Up to 25 are aligned." } }, "additionalProperties": false }arguments 14 linesdot_plot unknown never probed
Word-match dot plot between two sequences, on both strands, returned as diagonal RUNS rather than points. This is the view that shows what a single best alignment hides: internal repeats, tandem duplications, and inversions — an inversion appears as a run on the falling diagonal and as nothing at all in a normal pairwise alignment. Compare a sequence with itself to map its own repeats. Word size is chosen from the input lengths when you do not set one, because too short a word fills the plot with chance matches that the eye reads as homology.
{ "type": "object", "required": [ "a", "b" ], "properties": { "a": { "type": "string", "residues": "nt", "description": "First sequence (raw or FASTA). Max 200,000 nt." }, "b": { "type": "string", "residues": "nt", "description": "Second sequence. Pass the same sequence as \"a\" to find its internal repeats. Max 200,000 nt." }, "maxRuns": { "type": "integer", "default": 2000, "description": "Most runs to return, longest first." }, "wordSize": { "type": "integer", "maximum": 64, "minimum": 4, "description": "Exact-match word length. Omit to pick one from the sequence lengths." }, "bothStrands": { "type": "boolean", "default": true, "description": "Also search the reverse complement, which is what reveals inversions." }, "minRunLength": { "type": "integer", "default": 0, "description": "Drop runs shorter than this before returning. 0 = keep every run at least wordSize long." } }, "additionalProperties": false }arguments 41 linesidentity_matrix unknown never probed
Percent identity between every pair in a multiple alignment. Takes ALIGNED sequences — the output of multiple_sequence_alignment — because inferring an alignment here would bury the aligner's parameters inside a number that reads as a property of the sequences. Two percentages come back per pair: over columns where both have a residue (the usual figure), and over all columns including gaps. The gap between them is the warning — two sequences overlapping in 50 of 2,000 columns read 100% by the first measure and 2.5% by the second.
{ "type": "object", "required": [ "sequences" ], "properties": { "sequences": { "type": "string", "description": "Aligned FASTA (gaps as \"-\"), or an array of {id, sequence}. All rows must be the same length. Max 200 sequences." }, "caseSensitive": { "type": "boolean", "default": false, "description": "Treat upper and lower case as different residues. Off by default — soft-masking is not a mismatch." } }, "additionalProperties": false }arguments 18 linescrispr_offtarget_check unknown never probed
Screen a guide's protospacer for off-target sites (protospacer match + valid PAM, both strands) against a small curated set of common lab reference genomes (see genomesChecked) — NOT a whole human/mouse genome search. For SpCas9 with a 20 nt spacer each site also gets a Doench 2016 CFD score, so sites are ranked by predicted cut likelihood rather than by mismatch count alone, and the guide gets an aggregate specificity. Use this the same way primer_specificity is used: a useful sanity check within the covered organisms, not a clearance guarantee for a mammalian expression host. PREDICTED, NOT MEASURED. Best of the common off-target scores on the authors' GUIDE-Seq comparison, at Pearson r = 0.40 over 9 guides and 402 sites (vs CCTop 0.31, Hsu-Zhang 0.26) — a useful ranking, not a reliable magnitude. Weights were measured for SINGLE mismatches; multiple mismatches are multiplied, and Listgarten et al. 2018 note the training data never contained a mismatch and an alternative PAM together, so that combination is extrapolation. Valid for: SpCas9 with a 20 nt spacer, which is the only case scored — every other nuclease returns null rather than a number from the wrong enzyme's table. One locus, one cell line. Substitutions only: DNA/RNA bulges are neither searched nor scorable, and a low score is not a claim that a site is safe.
{ "type": "object", "required": [ "protospacer" ], "properties": { "nuclease": { "enum": [ "spcas9", "spcas9ng", "sacas9", "cas12a" ], "type": "string", "default": "spcas9", "description": "Nuclease id — determines the PAM pattern/side required at each candidate site." }, "protospacer": { "type": "string", "residues": "nt", "maxLength": 32, "description": "The guide's protospacer sequence, 5'→3' (no PAM). Max 32 nt — every supported nuclease uses a 20–23 nt guide." }, "maxMismatches": { "type": "integer", "default": 2, "maximum": 4, "minimum": 0, "description": "Mismatches tolerated between the protospacer and a candidate genomic site. Max 4 — a complete search seeds on maxMismatches+1 non-overlapping blocks, and past that the blocks are too short to be selective against a multi-Mb genome (a site that mismatched more would not be cut anyway)." } }, "additionalProperties": false }arguments 33 linescrispr_hdr_donor unknown never probed
Build an HDR donor (homology arms flanking an edit) from a target sequence and either an explicit edit window (editStart/editEnd) or a guide's cut site (guideStart/guideEnd/guideStrand/nuclease — SpCas9-family only; Cas12a's staggered cut needs an explicit editStart/editEnd). Also designs genotyping primers spanning the edit site on the original sequence (a real size-shift or sequencing target to confirm the edit), reusing the same primer-design engine as primer_design.
{ "type": "object", "required": [ "targetSequence", "replacement" ], "properties": { "editEnd": { "type": "integer", "description": "1-based inclusive end of the region being replaced; editEnd = editStart-1 denotes a pure insertion with nothing removed. Omit to derive from the guide's cut site." }, "blockPam": { "type": "boolean", "default": true, "description": "When a SpCas9-family guide is supplied and the edit does not already disrupt its PAM, fold a PAM-blocking mutation (silent when a CDS frame is given) into the donor so the edited allele can't be re-cut." }, "guideEnd": { "type": "integer", "description": "1-based forward-strand end of the guide's protospacer." }, "nuclease": { "enum": [ "spcas9", "spcas9ng", "sacas9", "cas12a" ], "type": "string", "default": "spcas9", "description": "Needed only when deriving the cut site from guideStart/guideEnd/guideStrand." }, "armLength": { "type": "integer", "default": 500, "description": "Homology arm length (bp) on each side. Use ~30–60 for an ssODN donor, ~500–1000 for a dsDNA donor plasmid." }, "editStart": { "type": "integer", "description": "1-based start of the region being replaced. Omit to derive from guideStart/guideEnd/guideStrand instead." }, "frameStart": { "type": "integer", "description": "Optional 1-based CDS reading-frame start; makes the PAM-blocking mutation synonymous where possible." }, "guideStart": { "type": "integer", "description": "1-based forward-strand start of the guide's protospacer (alternative to editStart/editEnd, for an insertion exactly at the cut site)." }, "guideStrand": { "enum": [ "+", "-" ], "type": "string", "description": "Strand the guide's protospacer is on." }, "replacement": { "type": "string", "default": "", "description": "Sequence to insert/substitute (\"\" for a pure deletion)." }, "targetSequence": { "type": "string", "residues": "nt", "description": "Nucleotide sequence (raw or FASTA; IUPAC accepted)." }, "designGenotypingPrimers": { "type": "boolean", "default": true, "description": "Also design a primer pair (on the original targetSequence) whose product spans the edit site." } }, "additionalProperties": false }arguments 74 linescrispr_ontarget unknown never probed
Score SpCas9 guides for on-target activity with Rule Set 3 (DeWeirdt et al., Nat Commun 2022) — the current successor to the Doench 2014 and CRISPRscan scores crispr_grna_design reports. Give a target sequence to find and score every NGG guide in it, or give 30-mer contexts directly. The tracrRNA MATTERS and is not cosmetic: Rule Set 3 models it as a feature, and the paper measures its accuracy dropping when the wrong one is specified. Returns a z-scored activity, which ranks guides against each other; it is not a percentage and not a probability of editing. PREDICTED, NOT MEASURED. Held out six datasets (23,629 context sequences) from training; Rule Set 3 (Sequence) had the highest Spearman correlation on three of the six. On a separate tiling library generated for the paper, with every spacer any model had seen removed, it significantly outperformed all other models (p < 0.002) when the correct tracrRNA was given. Calibration on that independent set: of the lowest-scoring guides, 87.7% / 74.9% / 82.0% landed in the bottom two activity quintiles (Hsu / Chen / DeWeirdt tracrRNA), and of the highest-scoring, 77.0% / 69.0% / 75.5% landed in the top two. No single held-out Spearman is quoted here because the paper reports it per gene as a distribution rather than as one figure, and inventing a headline number from a figure would be the fit-residual mistake in a different costume. Valid for: SpCas9 with an NGG PAM and a 20 nt spacer, scored over a 30-mer (4 nt upstream + spacer + PAM + 3 nt downstream) — nothing is padded, so a guide without that flank is skipped rather than estimated. Knockout activity in mammalian pooled screens with a U6/Pol III promoter; the authors expect it to generalize less well to Pol II-transcribed sgRNAs, and in vitro transcribed sgRNAs (as used in zebrafish) are known to be poorly predicted by models trained this way. The tracrRNA must be the one you will actually use. This is Rule Set 3 (Sequence) only: the Sequence+Target model, which adds 6.7% to the Spearman correlation on average, needs per-gene conservation and protein-domain lookups and is not implemented here.
{ "type": "object", "properties": { "tracr": { "enum": [ "Hsu2013", "Chen2013" ], "type": "string", "default": "Hsu2013", "description": "Which tracrRNA the guides will be paired with. Hsu2013 is the one in lentiCRISPRv2 and most published libraries; Chen2013 is the sgRNA(F+E) scaffold used by the Sanger/Yusa libraries. If you use the DeWeirdt (2020) tracrRNA, the paper reports Chen2013 as the better proxy — there is no DeWeirdt option in the model itself." }, "contexts": { "type": "array", "items": { "type": "string" }, "description": "30-mer contexts to score directly: 4 nt upstream + 20 nt spacer + PAM + 3 nt downstream. Give this OR `sequence`." }, "sequence": { "type": "string", "residues": "nt", "description": "Target DNA to find NGG guides in. Give this OR `contexts`." } }, "additionalProperties": false }arguments 27 lineselsa_capacity unknown never probed
Report how many promoters, sgRNA handles and neutral spacers are available at each maximum-shared-length threshold, and therefore the longest extra-long sgRNA array that can be built without reusing a part. Ask this before designing: the answer is a property of the measured parts collection, not of your guides, and it is the constraint that decides the design. Deterministic — it is a selection over a fixed table.
{ "type": "object", "required": [], "properties": { "lmax": { "type": "integer", "maximum": 40, "minimum": 8, "description": "Report a single threshold. Omit to get the whole curve from 8 to 24." } }, "additionalProperties": false }arguments 13 lineselsa_design unknown never probed
Build a multiplexed CRISPR array that expresses many sgRNAs from one cassette and shares no long stretch with itself. Twenty sgRNAs built the obvious way carry twenty copies of the same Cas9 scaffold, promoter and terminator — a construct that recombines in the cell and that synthesis vendors refuse — so this draws each transcription unit's parts from the measured non-repetitive collection of Reis et al. (2019), selecting ACROSS promoters, handles and spacers at once rather than within each type, then re-measures the assembled molecule for repeats the junctions created. Returns the sequence, an annotated GenBank file and the pool usage. Takes guides; it does not choose or score them — use crispr_grna_design and crispr_offtarget_check for that.
{ "type": "object", "required": [ "guides" ], "properties": { "lmax": { "type": "integer", "default": 12, "maximum": 40, "minimum": 8, "description": "Longest stretch any two parts in the array may share, in bp (default 12). Lower is more stable and leaves fewer parts to choose from: the handle pool offers 12 at lmax 12, 18 at 15 and 24 at 20. Run elsa_capacity first." }, "name": { "type": "string", "description": "LOCUS name for the GenBank output." }, "guides": { "type": "array", "items": { "type": "string" }, "description": "The 20 nt protospacers, in array order, WITHOUT their PAM. Strings, or {name, sequence} objects to label each unit. Max 27 — the size of the handle collection." }, "insulate": { "type": "boolean", "default": true, "description": "Place a neutral spacer between transcription units. Turning it off frees the spacer pool from the selection, which can let a longer array fit at a low lmax." }, "includeGenbank": { "type": "boolean", "default": true, "description": "Return the annotated GenBank file." } }, "additionalProperties": false }arguments 37 linesparse_genbank unknown never probed
Parse a GenBank flat file into its locus, definition, features and sequence. An EMBL / ENA flat file is accepted too — the same INSDC record in a different layout — and reported with sourceFormat "embl".
{ "type": "object", "required": [ "text" ], "properties": { "text": { "type": "string", "description": "A GenBank flat file (LOCUS … FEATURES … ORIGIN … //)." } }, "additionalProperties": false }arguments 13 linessequence_format_convert unknown never probed
Convert between FASTA and GenBank (whole sequence, CDS or protein), or export to TSV.
{ "type": "object", "required": [ "input" ], "properties": { "to": { "enum": [ "fasta", "fasta-cds", "fasta-protein", "genbank", "tsv", "snapgene" ], "type": "string", "default": "fasta", "description": "Output format. fasta-cds / fasta-protein extract CDS features (GenBank input only). GenBank in and 'genbank' out rewrites the record with its features, qualifiers and topology intact — it is a rewrite, not a re-annotation. 'snapgene' writes a binary SnapGene .dna file, returned base64 in `fileBase64` rather than in `output`; it takes ONE record, because a .dna holds one molecule." }, "from": { "enum": [ "auto", "fasta", "genbank" ], "type": "string", "default": "auto", "description": "Input format; 'auto' sniffs it from the first meaningful line." }, "input": { "type": "string", "description": "A FASTA or GenBank record to convert." } }, "additionalProperties": false }arguments 36 linesparse_sanger_trace unknown never probed
Decode a Sanger ABIF (.ab1 / .abi) chromatogram: base calls, per-base quality, the four dye-channel traces, peak locations, and the run's own labels (sample name, well, plate, instrument, run start).
{ "type": "object", "required": [ "fileBase64" ], "properties": { "fileName": { "type": "string", "description": "Optional original file name (echoed back)." }, "fileBase64": { "type": "string", "description": "The binary ABIF (.ab1 / .abi) trace file, base64-encoded." }, "includeTraces": { "type": "boolean", "default": false, "description": "Include the four raw dye-channel arrays and peakLocations. They are 93% of the response — a 900-base read is 122 kB with them and 8 kB without (measured) — and they are only useful for DRAWING the chromatogram. Everything you would reason about (base calls, quality, the run's labels) is returned either way, so leave this off unless you are rendering." } }, "additionalProperties": false }arguments 22 linessanger_vs_reference unknown never probed
Align a Sanger ABIF read to a reference and report identity plus every mismatch, insertion and deletion.
{ "type": "object", "required": [ "reference" ], "properties": { "read": { "type": "string", "residues": "nt", "description": "Sanger read as FASTA or raw text (alternative to uploading an ABIF trace). Also the per-record field for plate-batch runs via /api/v1/batch." }, "fileName": { "type": "string", "description": "Optional original file name (echoed back)." }, "reference": { "type": "string", "residues": "nt", "description": "Expected reference sequence (FASTA or raw)." }, "fileBase64": { "type": "string", "description": "The binary ABIF (.ab1 / .abi) trace file, base64-encoded." }, "minCoverage": { "type": "number", "default": 0.9, "description": "Fraction of the reference the read must span before a PASS is meaningful; below this the verdict is 'ambiguous_low_coverage' regardless of identity. Lower it when the reference is intentionally just the region/junction being checked." } }, "additionalProperties": false }arguments 32 linesparse_snapgene unknown never probed
Read a SnapGene .dna file: sequence, topology, every feature with its span, strand, display color and qualifiers (spliced and origin-spanning features kept as such), and the saved primer list.
{ "type": "object", "required": [ "fileBase64" ], "properties": { "fileName": { "type": "string", "description": "Optional original file name (echoed back)." }, "fileBase64": { "type": "string", "maxLength": 43000000, "description": "The binary SnapGene .dna file, base64-encoded. A `data:...;base64,` prefix is accepted." }, "featureLimit": { "type": "integer", "default": 2000, "maximum": 2000, "minimum": 1, "description": "Cap on features returned (max 2000). featureCount always reports the true total and `truncated` says whether the list was cut." }, "includeSequence": { "type": "boolean", "default": true, "description": "Include the full sequence. Turn it off to ask what is IN a construct without moving the bases: a 250 kb BAC is 244 kB of the response and length/topology/features answer most questions without it." } }, "additionalProperties": false }arguments 30 linessanger_assemble unknown never probed
Assemble two or more Sanger reads into a contig WITHOUT a reference sequence — the forward/reverse pair of one insert, or a set of tiling reads. Orientation is worked out from the overlaps, ends are quality-trimmed, and the consensus is quality-weighted. Reports depth and agreement per position, every position where the reads disagree (including a base only one read has), and any read that overlapped nothing. Use sanger_vs_reference instead when you already know what the sequence should be.
{ "type": "object", "properties": { "fasta": { "type": "string", "residues": "nt", "description": "Alternative to `reads`: a multi-record FASTA of the reads. No quality, so no end trimming." }, "reads": { "type": "array", "items": { "type": "object" }, "description": "The reads, as [{name, sequence, quality?}]. `quality` is a per-base Phred array the same length as `sequence`; without it the read still assembles but its ends are NOT trimmed, which the result says." }, "noTrim": { "type": "boolean", "default": false, "description": "Assemble the reads exactly as given, with no quality trimming." }, "minOverlap": { "type": "integer", "default": 30, "description": "Shortest overlap that may join two reads." }, "minIdentity": { "type": "number", "default": 85, "description": "Lowest percent identity an overlap may have." }, "trimThreshold": { "type": "number", "description": "Phred threshold for end-trimming. Ignored for reads with no quality array." } }, "additionalProperties": false }arguments 37 linescharacterize_sequence unknown never probed
One-paste 'tell me everything': auto-detects DNA/RNA/protein, then reports composition, ORFs, single-cutter enzymes, end primers or protein properties, plus a BLAST link.
{ "type": "object", "required": [ "sequence" ], "properties": { "maxOrfs": { "type": "integer", "default": 8, "description": "Maximum number of ORFs to return, longest first." }, "minOrfAa": { "type": "integer", "default": 40, "description": "Minimum ORF length in amino acids (nucleotide input only)." }, "sequence": { "type": "string", "residues": "any", "description": "Nucleotide or protein sequence (raw or FASTA; IUPAC accepted). The alphabet is detected." }, "endPrimerLength": { "type": "integer", "default": 20, "description": "Length of the naive end primers taken from each end." } }, "additionalProperties": false }arguments 29 linessequence_report unknown never probed
One-click DNA analysis: composition, ORFs, restriction-enzyme scan (single cutters) and end-primer Tm composed into a single report with a copyable text block.
{ "type": "object", "required": [ "sequence" ], "properties": { "maxOrfs": { "type": "integer", "default": 10, "description": "Maximum number of ORFs to return, longest first." }, "minOrfAa": { "type": "integer", "default": 50, "description": "Minimum ORF length in amino acids." }, "sequence": { "type": "string", "residues": "nt", "description": "Nucleotide sequence (raw or FASTA; IUPAC accepted)." }, "endPrimerLength": { "type": "integer", "default": 20, "description": "Length of the naive end primers taken from each end." } }, "additionalProperties": false }arguments 29 linescpg_islands unknown never probed
Find CpG islands by either published definition: Gardiner-Garden & Frommer 1987 (GC > 50%, observed/expected CpG > 0.6, >= 200 bp — the original, which also calls many Alu repeats) or Takai & Jones 2002 (GC >= 55%, obs/exp >= 0.65, >= 500 bp — written to exclude them). Windows are merged only where the merged region STILL meets the criteria, so every island returned satisfies the definition it is reported under. Reports the CpG DINUCLEOTIDE count separately from GC content, because conflating the two is the usual way this number goes wrong.
{ "type": "object", "required": [ "sequence" ], "properties": { "preset": { "enum": [ "gardiner-garden", "takai-jones" ], "type": "string", "default": "gardiner-garden", "description": "Which published criteria to apply. \"gardiner-garden\": Gardiner-Garden & Frommer 1987 (GC > 50%, obs/exp > 0.6, >= 200 bp; thresholds strict, as the paper states them) \"takai-jones\": Takai & Jones 2002 (GC >= 55%, obs/exp >= 0.65, >= 500 bp; excludes most Alu)" }, "mergeGap": { "type": "integer", "default": 100, "description": "Join passing regions closer than this, when the joined region still passes. Takai & Jones use 100." }, "minGcPct": { "type": "number", "description": "Override the preset's GC threshold, 0-100." }, "sequence": { "type": "string", "residues": "nt", "description": "DNA to scan (raw or FASTA). Max 5,000,000 bases." }, "minLength": { "type": "integer", "description": "Override the preset's minimum island length, bp." }, "minObsExp": { "type": "number", "description": "Override the preset's observed/expected CpG threshold." }, "windowSize": { "type": "integer", "default": 200, "description": "Scanning window in bp. 200 is Takai & Jones' window, and it is used for both presets so the two differ only in their thresholds (Gardiner-Garden & Frommer's 1987 paper scanned 100 bp windows)." } }, "additionalProperties": false }arguments 45 linesparse_gff3 unknown never probed
Read a GFF3 annotation file: every feature with its 1-based inclusive coordinates, strand, phase, score and decoded attributes, plus any sequences from an embedded ##FASTA section. GFF3 usually carries NO sequence — it annotates a separate FASTA, joined on the first column — so the result says which of the two it was handed. Give `sequence` (or let an embedded ##FASTA supply it) to also get the record as GenBank, readable by every other tool here. Percent-escapes are decoded, `.` is read as absent rather than zero, and a feature repeated across lines keeps both lines.
{ "type": "object", "required": [ "text" ], "properties": { "text": { "type": "string", "description": "GFF3 text. Up to 200,000 feature lines." }, "limit": { "type": "integer", "default": 500, "description": "Most features to return in the table (1-5000)." }, "seqid": { "type": "string", "description": "Which sequence's features to return, when the file covers several. Defaults to the first." }, "sequence": { "type": "string", "residues": "nt", "description": "The DNA these annotations describe, when the file has no ##FASTA section. Enables the GenBank output." }, "asGenbank": { "type": "boolean", "default": true, "description": "Also return the record as a GenBank flat file, when a sequence is available." } }, "additionalProperties": false }arguments 32 linesblast_submit unknown never probed
Submit a sequence to NCBI BLAST and get a request id back immediately — poll it with blast_poll. The program is inferred from the sequence (nucleotide to blastn, protein to blastp) unless you name one, and a query whose type does not match the named program is refused rather than silently returning nothing. Databases: blastn: nt, refseq_rna (default nt); blastx: nr (default nr); blastp: nr, swissprot (default nr); tblastn: nt (default nt). Up to 20,000 residues. Searches typically take 20-60 seconds; NCBI asks that a single search is polled no more than once a minute.
{ "type": "object", "required": [ "sequence" ], "properties": { "evalue": { "type": "number", "description": "Report only hits at or below this expect value. NCBI's default is 10." }, "program": { "enum": [ "blastn", "blastp", "blastx", "tblastn" ], "type": "string", "description": "BLAST program. Omit to infer from the sequence: blastn for nucleotide, blastp for protein. blastx translates a nucleotide query and searches proteins; tblastn searches translated nucleotide databases with a protein query." }, "database": { "type": "string", "description": "Database to search. Omit for the program's default. blastn: nt, refseq_rna (default nt); blastx: nr (default nr); blastp: nr, swissprot (default nr); tblastn: nt (default nt)." }, "sequence": { "type": "string", "description": "DNA or protein to search, raw or FASTA. Up to 20,000 residues." }, "megablast": { "type": "boolean", "default": true, "description": "blastn only. Megablast (the default) finds near-identical sequences and is what identifies a clone; set false for a slower search that also finds diverged ones. Left unset, a query shorter than megablast's 28-base seed runs as plain blastn, since megablast cannot seed it at all." }, "hitlistSize": { "type": "integer", "default": 20, "description": "Most database sequences to report (1-100)." } }, "additionalProperties": false }arguments 41 linesblast_poll unknown never probed
Check a BLAST search submitted with blast_submit. Returns {ready:false} while it is still running; once ready, returns each hit's accession, title, organism, best HSP (bit score, expect, percent identity, span on both query and subject) and the percentage of the QUERY it covers, with overlapping HSPs merged so coverage cannot exceed 100%. A request id NCBI no longer recognises is reported as either a typo or an expired search, which is the same answer it gives for both.
{ "type": "object", "required": [ "rid" ], "properties": { "rid": { "type": "string", "description": "The request id returned by blast_submit." } }, "additionalProperties": false }arguments 13 linesod600_cells unknown never probed
Convert an OD600 reading to a cell density and a total cell count, correcting for the optical path and any dilution, and flagging the two things that silently make the number wrong: a reading above the linear range (a dense culture reads LOW), and a plate-reader path length assumed to be a cuvette's 1 cm. Also plans a back-dilution to a target OD. The cells-per-OD factor is a convention, not a constant — it varies with strain, growth phase and instrument, so pass factorPerOd when you have calibrated against plate counts.
{ "type": "object", "required": [ "od600" ], "properties": { "od600": { "type": "number", "default": 0.5, "description": "The reading off the spectrophotometer." }, "organism": { "enum": [ "ecoli", "scerevisiae", "ppastoris" ], "type": "string", "default": "ecoli", "description": "Supplies the cells-per-OD factor. Ignored when factorPerOd is given." }, "targetOd": { "type": "number", "default": 0, "description": "Optional: plan a back-dilution to this OD. 0 = skip." }, "volumeMl": { "type": "number", "default": 0, "description": "Culture volume, for a total cell count. 0 = not given." }, "factorPerOd": { "type": "number", "description": "Your own calibration: cells/mL at OD600 = 1.0 in a 1 cm path. Overrides organism." }, "pathLengthCm": { "type": "number", "default": 1, "description": "Optical path of the reading. A cuvette is 1 cm; 200 µL in a 96-well flat plate is about 0.58 cm." }, "dilutionFactor": { "type": "number", "default": 1, "description": "Dilution done before reading (2 means the sample was diluted 1:2)." }, "targetVolumeMl": { "type": "number", "default": 50, "description": "Final volume for the back-dilution plan." } }, "additionalProperties": false }arguments 53 linesqpcr_ddct unknown never probed
Relative quantification from Ct values: ΔCt, ΔΔCt and fold change, with the standard error propagated from replicates. Picks the method from the amplicon efficiencies rather than leaving it to you — Livak's 2^-ΔΔCt when both are 100% efficient, the Pfaffl efficiency-corrected ratio when they are not, since running Livak over amplicons that do not qualify is the failure this tool exists to prevent. Reports what Livak would have said, so the size of that difference is visible.
{ "type": "object", "required": [ "sampleTarget", "sampleReference", "controlTarget", "controlReference" ], "properties": { "sampleTarget": { "type": "array", "items": { "type": "number" }, "description": "Ct values for the gene of interest in the treated/test sample. Replicates as a list." }, "controlTarget": { "type": "array", "items": { "type": "number" }, "description": "Ct values for the gene of interest in the calibrator/control sample." }, "sampleReference": { "type": "array", "items": { "type": "number" }, "description": "Ct values for the reference (housekeeping) gene in the same sample." }, "controlReference": { "type": "array", "items": { "type": "number" }, "description": "Ct values for the reference gene in the control sample." }, "targetEfficiency": { "type": "number", "default": 2, "description": "Per-cycle amplification fold for the target amplicon. 2.0 = 100%. From a standard curve, E = 10^(-1/slope)." }, "referenceEfficiency": { "type": "number", "default": 2, "description": "Per-cycle amplification fold for the reference amplicon. 2.0 = 100%." } }, "additionalProperties": false }arguments 50 linescentrifuge_conversion unknown never probed
Convert between rotor speed (RPM) and relative centrifugal force (×g) for a given rotor radius, in either direction. The conversion is exact physics — RCF = ω²r/g — and the only judgement in it is which radius: a protocol's ×g conventionally means the rotor's MAXIMUM radius, and using the wrong one scales the force by the ratio of the two.
{ "type": "object", "required": [ "radiusCm" ], "properties": { "rcf": { "type": "number", "description": "Relative centrifugal force in ×g. Give this OR rpm." }, "rpm": { "type": "number", "description": "Speed in revolutions per minute. Give this OR rcf." }, "radiusCm": { "type": "number", "description": "Rotor radius in cm — the maximum radius, from the rotor manual. Required: there is no typical rotor to assume." } }, "additionalProperties": false }arguments 21 linesprotein_annotate_submit unknown never probed
Submit a protein sequence to EBI InterProScan for domain architecture, family and GO-term annotation. Returns a jobId immediately — the job itself takes minutes; poll it with protein_annotate_poll.
{ "type": "object", "required": [ "sequence" ], "properties": { "appl": { "type": "string", "description": "Restrict to one member database (e.g. \"PfamA\"); omit to run EBI's defaults across all of them." }, "goterms": { "type": "boolean", "default": true, "description": "Include GO-term cross-references." }, "sequence": { "type": "string", "description": "Protein sequence, one-letter code (FASTA header, if any, is stripped)." } }, "additionalProperties": false }arguments 22 linessolution_prep unknown never probed
How much to weigh out for a target molarity and volume: mass = C × V × MW. The molar mass comes from a named reagent's molecular FORMULA (computed, not transcribed) or from a value you supply. A bare name matching two hydration states is refused with both named rather than resolved to a guess — EDTA disodium dihydrate against the free acid is a 27% error that leaves a solution looking exactly like a solution.
{ "type": "object", "required": [ "concentration", "volume" ], "properties": { "volume": { "type": "number", "default": 100, "description": "Volume to make." }, "reagent": { "type": "string", "description": "Reagent name as printed on the bottle, hydration state included (27 known). Ignored when molarMass is given." }, "molarMass": { "type": "number", "description": "Formula weight in g/mol. Overrides reagent." }, "volumeUnit": { "enum": [ "L", "mL", "uL" ], "type": "string", "default": "mL", "description": "Unit for volume." }, "concentration": { "type": "number", "default": 1, "description": "Target concentration." }, "concentrationUnit": { "enum": [ "M", "mM", "uM", "nM" ], "type": "string", "default": "M", "description": "Unit for concentration." } }, "additionalProperties": false }arguments 49 linessession_create unknown never probed
Start a scratch session that holds several named sequences/values (e.g. vector, insert, forward/reverse primer) for use across multiple tool calls via session_run, instead of re-pasting them into every call. Sessions expire after 24 hours.
{ "type": "object", "required": [], "properties": { "entries": { "type": "object", "description": "Initial named entries, e.g. {\"vector\": \"...\", \"insert\": \"...\"}. Optional — you can also add entries later with session_set.", "additionalProperties": { "type": "string" } } }, "additionalProperties": false }arguments 14 linessession_run unknown never probed
Run any SeqBench tool, resolving selected arguments from a session's named entries instead of pasting them inline, and optionally store selected result fields back into the session by name. This is the main way to chain a multi-part design (vector + insert + primers) across calls without shuttling raw sequences through your own context.
{ "type": "object", "required": [ "sessionId", "tool" ], "properties": { "args": { "type": "object", "description": "Additional literal arguments, merged with the ones resolved from the session.", "additionalProperties": true }, "tool": { "type": "string", "description": "Name of any non-meta SeqBench tool (not batch, workflow, or another session_* tool)." }, "sessionId": { "type": "string" }, "writeBack": { "type": "object", "description": "Map of { resultFieldName: sessionEntryName } — stores selected fields of the result back into the session under these names.", "additionalProperties": { "type": "string" } }, "fromSession": { "type": "object", "description": "Map of { toolArgName: sessionEntryName } — resolves each named tool argument from the session before running.", "additionalProperties": { "type": "string" } } }, "additionalProperties": false }arguments 36 linessequence_fetch unknown never probed
Fetch a public DNA/protein record by accession from NCBI Nucleotide, NCBI Protein, UniProt, or Ensembl (e.g. NM_000546, NP_000537, P04637, ENSG00000141510). Only the accession is sent upstream. Use sequence_search first if you only know a gene/organism name, not an accession. For an Ensembl transcript ID this returns spliced cDNA; for a gene ID it returns the full genomic locus (introns included) — Ensembl's own default for each ID type.
{ "type": "object", "required": [ "accession" ], "properties": { "db": { "enum": [ "auto", "nucleotide", "protein", "uniprot", "ensembl" ], "type": "string", "default": "auto", "description": "Database to query; auto-detects from the accession format." }, "format": { "enum": [ "fasta", "genbank" ], "type": "string", "default": "fasta", "description": "Output format (GenBank is only available for NCBI accessions — UniProt and Ensembl are FASTA-only)." }, "accession": { "type": "string", "description": "GenBank/RefSeq accession (e.g. NM_000546), UniProtKB accession (e.g. P04637), or Ensembl stable ID (e.g. ENSG00000141510, ENST00000335137)." } }, "additionalProperties": false }arguments 34 linessequence_search unknown never probed
Resolve a gene/organism name — or a raw NCBI search term — to candidate accessions, instead of guessing one. Returns up to maxResults hits (accession, title, organism); pass the accession you want to sequence_fetch.
{ "type": "object", "required": [], "properties": { "db": { "enum": [ "nucleotide", "protein" ], "type": "string", "default": "nucleotide" }, "gene": { "type": "string", "description": "Gene symbol/name, e.g. \"BRCA1\". Combined with organism (if given) into a search term." }, "term": { "type": "string", "description": "Raw NCBI search term (advanced) — overrides gene/organism when given, e.g. \"BRCA1[gene] AND Homo sapiens[orgn]\"." }, "organism": { "type": "string", "description": "Organism name, e.g. \"Homo sapiens\". Optional; narrows the gene search." }, "maxResults": { "type": "integer", "default": 5, "maximum": 20, "minimum": 1, "description": "Up to 20." } }, "additionalProperties": false }arguments 34 linesplasmid_full_report unknown never probed
One combined view of 'what is this plasmid': recognized common features (from plasmid_annotate), backbone identity / possible chimera (from plasmid_identify), and — the two crossed together — any region that neither a curated backbone nor a recognized common feature explains. That last list is a triage signal (an unusual insert, an unannotated part, or worth a closer look), not a defect finding: a real gene-of-interest legitimately has no curated-feature match.
{ "type": "object", "required": [ "sequence" ], "properties": { "topN": { "type": "integer", "default": 5, "description": "How many top-ranked backbone candidates to report." }, "circular": { "type": "boolean", "default": true, "description": "Treat the query as a circular molecule (most plasmids are)." }, "sequence": { "type": "string", "residues": "nt", "description": "Nucleotide sequence (raw or FASTA; IUPAC accepted)." } }, "additionalProperties": false }arguments 24 linesplasmid_dossier unknown never probed
Answer the question someone holding an unlabelled tube actually has, rather than returning another feature list: which antibiotic to select on, which host will carry it and at roughly what copy number, which curated backbone it resembles, and what on it will bite you later (duplicate markers, two origins for the same host, internal Type IIS sites that stop it being a Golden Gate part, long direct repeats a recA+ host can recombine out). Reads features from an annotated GenBank record when you paste one, otherwise runs the built-in signature scan. EVERY ABSENCE TRAVELS WITH THE VOCABULARY IT WAS DECIDED AGAINST: an empty marker list means nothing matched the families this screen knows, never that the plasmid cannot be selected — run plasmid_deep_annotate, whose library is far larger, before concluding that.
{ "type": "object", "required": [ "sequence" ], "properties": { "circular": { "type": "boolean", "default": true, "description": "Treat the query as a circular molecule (most plasmids are)." }, "sequence": { "type": "string", "residues": "nt", "description": "Nucleotide sequence (raw or FASTA; IUPAC accepted)." }, "minRepeatLength": { "type": "integer", "default": 30, "description": "Shortest direct repeat (bp) to raise as a recombination hazard. Below ~20 bp chance matches multiply and recombination has little to work with." }, "goldenGateEnzymes": { "type": "array", "items": { "type": "string" }, "description": "Type IIS enzymes you intend to assemble with (e.g. [\"BsaI\"]). Internal sites are ALWAYS reported in typeIISSites — random sequence carries them and so does nearly every real plasmid — but they only become a hazard for an enzyme named here, so the hazard list stays worth reading." } }, "additionalProperties": false }arguments 31 lineskasp_primer_design unknown never probed
Design KASP/ARMS allele-specific genotyping primers for a SNP: two allele-specific forward primers differing only at the 3' terminal base (one per allele), each with the standard KASP universal tail (FAM for allele A, HEX for allele B), a deliberate internal ARMS secondary mismatch near the 3' end whose strength complements that primer's own natural allele mismatch (strong↔weak), and one common downstream reverse primer sized to a chosen amplicon range. Because a forward primer reads the antisense strand, each primer's 3' base sits opposite the complement of the other allele, so the two primers get different mismatch classes and are reported separately (graded from the measured PCR yields in Kwok et al. 1990). Reuses the site's nearest-neighbor Tm engine.
{ "type": "object", "required": [ "target", "snpPosition", "alleleA", "alleleB" ], "properties": { "target": { "type": "string", "residues": "nt", "description": "Nucleotide sequence (raw or FASTA; IUPAC accepted)." }, "alleleA": { "type": "string", "residues": "nt", "description": "First allele (single base) — gets the FAM tail." }, "alleleB": { "type": "string", "residues": "nt", "description": "Second allele (single base) — gets the HEX tail." }, "maxAmplicon": { "type": "integer", "default": 150, "description": "Maximum amplicon length for the common reverse primer." }, "minAmplicon": { "type": "integer", "default": 60, "description": "Minimum amplicon length for the common reverse primer." }, "snpPosition": { "type": "integer", "minimum": 18, "description": "1-based position of the SNP on the forward strand. Must be 18 or greater: the allele-specific primers end on the SNP, so they need at least 17 bp of upstream template to build a core from." }, "targetCoreTm": { "type": "number", "default": 56, "description": "Target Tm (°C) for the allele-specific primer core (before the universal tail)." }, "addSecondaryMismatch": { "type": "boolean", "default": true, "description": "Engineer the internal ARMS destabilizing mismatch near the 3' end." } }, "additionalProperties": false }arguments 52 linesrna_fold unknown never probed
Predict an RNA secondary structure by minimum free energy (MFE) using a Zuker dynamic program with Turner 1999 nearest-neighbor stacking energies (no pseudoknots). Returns the dot-bracket structure, the estimated MFE (kcal/mol), and the list of base pairs. A from-scratch, in-browser implementation (there is no usable browser ViennaRNA); the simplified loop energy model makes the MFE a good comparative estimate, not a lab-grade absolute. PREDICTED, NOT MEASURED. No held-out skill statistic is claimed for this implementation. The loop model omits terminal mismatches, dangling ends, coaxial stacking and special hairpins that ViennaRNA and RNAstructure include, so the MFE is a comparative estimate between candidates rather than a lab-grade absolute. Valid for: a single strand up to 600 nt at a fixed 37 °C. No pseudoknots, no two-strand hybridization, and no temperature dependence — a structure predicted here is not a structure at your annealing temperature.
{ "type": "object", "required": [ "sequence" ], "properties": { "sequence": { "type": "string", "residues": "nt", "description": "Nucleotide sequence (raw or FASTA; IUPAC accepted)." } }, "additionalProperties": false }arguments 14 linesrbs_predict unknown never probed
Predict the translation initiation rate at each start codon in a bacterial mRNA using OSTIR, the open-source continuation of the Salis lab RBS Calculator, with ViennaRNA free energies. Returns the predicted rate plus the full thermodynamic breakdown (16S rRNA:mRNA hybridization, mRNA unfolding, spacing, standby site, start-codon binding) for every start codon found. Rates are on an arbitrary scale — compare them as ratios, not as absolute expression levels. Runs ViennaRNA on a shared service and is therefore rate limited (see 429/503). PREDICTED, NOT MEASURED (Spearman ρ = 0.39 on two 5' UTR datasets it was not fitted to). Spearman ρ = 0.39 against measured expression on two 5' UTR datasets it was not fitted to (Gilliot & Gorochowski, Nucleic Acids Res 2024;52(13):e58); reproduced in this repo at ρ = 0.509 on an independent leave-one-context-out split over 194,636 measurements, and at a mean ρ = 0.62 over fifteen further measurement systems it was not fitted to — six species, four reporters, three readouts — on which every learned model tried here scored BELOW it (scripts/rbs-eval) — above the published figure because 65,841 rows of that compilation record no measurement at all (fluorescence mean and s.d. both exactly 0) and are excluded here rather than scored as the weakest expression observed. The widely quoted 53% within 2-fold / 91% within 10-fold are calibration residuals on the fitting set, not held-out validation. Valid for: translation INITIATION only, in E. coli-like Gram-negative hosts (the model is parameterized on the E. coli anti-Shine-Dalgarno sequence). Rankings within one construct context; the absolute value has no units and no meaning.
{ "type": "object", "required": [ "sequence" ], "properties": { "end": { "type": "number", "description": "Optional 1-based position; only consider start codons beginning at or before it." }, "start": { "type": "number", "description": "Optional 1-based position; only consider start codons beginning at or after it." }, "sequence": { "type": "string", "description": "mRNA sequence, raw or FASTA — the 5' UTR plus at least the start of the CDS. DNA (T) and RNA (U) are both accepted and scored identically. A, C, G, T/U only. Max 10,000 nt." }, "antiShineDalgarno": { "type": "string", "description": "Optional anti-Shine-Dalgarno sequence (the 16S rRNA 3' end) to model a non-E. coli host. Omit to use OSTIR's own E. coli default." } }, "additionalProperties": false }arguments 25 linessequencing_readback_verify unknown never probed
Align raw Sanger or NGS reads (FASTA or FASTQ) back onto a claimed reference sequence using minimap2, and report per-read mapping identity plus exact variant positions (substitutions/insertions/deletions), with a consensus view across reads and a corrected consensus sequence (the reference with every consensus-supported edit applied). Each alignment also reports how much of the READ was used (queryCoveragePct/clippedBases), since identity is measured over the aligned portion only and a partially-used read would otherwise score perfectly. Set circular: true for a plasmid so reads crossing the reference's arbitrary linear start are aligned through the join rather than cut short at it. Also calls STRUCTURAL variants from split alignments — a large deletion, tandem duplication, inversion or backbone rearrangement never appears as a run of mismatches, only as one read aligning at several distant reference positions, so per-base calling reports a perfect clone — and returns a coverage depth profile with the regions no read reached at all, since "never read" is not "correct". On a circular reference one junction cannot always tell an event of length d from one of length referenceLength − d the other way round; where the read's own blocks and the coverage profile settle it they do, and where they do not the call carries an alternateInterpretation with the other reading rather than presenting one as a finding. Set platform (nanopore/pacbio/illumina/sanger) to pick minimap2's preset; the preset used is reported back. Complements verify_construct/verify_assembly: those re-derive what a design SHOULD produce from its own stated inputs; this checks what a real sequencer actually read back.
{ "type": "object", "required": [ "reference", "reads" ], "properties": { "reads": { "type": "string", "description": "Raw reads in FASTA or FASTQ format (auto-detected). Up to 2000 reads / 5,000,000 total bp per call." }, "circular": { "type": "boolean", "default": false, "description": "Treat the reference as a circular molecule (plasmid). Reads that straddle its arbitrary linear start are then aligned right through the join instead of being cut short there, so variants in the part that would otherwise be clipped away are actually called. Turn this on for whole-plasmid data — the reads begin wherever the molecule was cut, so most of them cross the join. Reads longer than the reference still get clipped. It also governs structural-variant calling: on a circle an origin-crossing read is contiguous, and only this flag lets it be told apart from a whole-reference duplication." }, "platform": { "enum": [ "auto", "nanopore", "pacbio", "illumina", "sanger" ], "type": "string", "default": "auto", "description": "Read type, which selects minimap2's alignment preset. \"auto\" (the default) passes no preset and uses minimap2's own defaults — whose parameters happen to be map-ont's, so nanopore data is already handled; setting \"nanopore\" makes that explicit and pins it. \"pacbio\" uses map-hifi and \"illumina\" uses sr, both of which materially change the result: under the ONT defaults gaps are cheap, so on accurate reads a cluster of mismatches can be reported as a spurious indel. \"sanger\" uses map-hifi with the minimum alignment score returned to 80, because map-hifi's own floor of 200 was chosen for 10-25 kb reads and would leave a short or partly-failed Sanger read unmapped. The preset actually used is reported back as minimap2Preset/alignerArgs so a run can be reproduced. Names are matched ignoring case and punctuation, and the obvious aliases resolve (\"ONT\" and \"map-ont\" to nanopore, \"HiFi\" to pacbio, \"sr\" to illumina); anything unrecognized is rejected rather than silently treated as \"auto\"." }, "reference": { "type": "string", "residues": "nt", "description": "The claimed/expected reference — bare bases, FASTA, or a whole GenBank record. Pass the GenBank record (your own map) to get consequences: every consensus edit is then placed against the features, so the answer reads \"silent in AmpR\" or \"premature STOP at codon 41 of your CDS\" instead of only a position and a base. Bare bases still work and simply return no consequences." }, "minSvLength": { "type": "integer", "default": 50, "description": "Smallest structural variant to report, in bp (default 50). Below this the per-base variant caller already reports the event from inside a single alignment, and on nanopore data the range is mostly the error profile." }, "minSvSupport": { "type": "integer", "default": 3, "description": "Distinct reads that must agree on the same breakpoint before a structural variant (large deletion, duplication, inversion, insertion) is reported. Default 3 — stricter than minSupportingReads on purpose: a single split read is a library-prep chimera or a mapping artifact far more often than it is biology, and chimeras are common enough that two agreeing by chance is likelier than two matching base errors." }, "minSupportingReads": { "type": "integer", "default": 2, "description": "Minimum number of reads agreeing on a variant position for it to count as a consensus (candidate real) variant rather than single-read noise." }, "breakpointTolerance": { "type": "integer", "default": 50, "description": "How far apart two reads' breakpoints may sit and still count as the same event, in bp (default 50). Long-read breakpoints are fuzzy, and microhomology at a real junction moves the split legitimately." } }, "additionalProperties": false }arguments 56 lineswhole_plasmid_verify unknown never probed
Compare a whole-plasmid sequencing CONSENSUS (the single circular FASTA a nanopore plasmid service returns) against the design it was supposed to be, and say whether they are the same molecule. Finds the rotation and strand itself — an assembler starts the circle wherever it landed and half the time returns the reverse complement, so the two almost never line up as written — then reports every difference in the DESIGN's own coordinates. Each difference carries the length of the identical-base run it sits in, because a 1 bp indel inside a homopolymer is both the commonest long-read basecalling artefact and what a real slippage mutation looks like, and a bare difference list cannot tell them apart. Pass the design as an annotated GenBank record and every difference is also read against its features: silent, missense with the codon number, or a premature stop. Complements sequencing_readback_verify, which aligns raw READS through minimap2; this one needs no reads and no sidecar.
{ "type": "object", "required": [ "design", "consensus" ], "properties": { "design": { "type": "string", "description": "What you meant to build: raw bases, FASTA, or your annotated GenBank record. An annotated record is what turns a position into a consequence." }, "circular": { "type": "boolean", "default": true, "description": "Treat both as circular (the default, and right for a plasmid). The consensus is then rotated and, if needed, reverse-complemented into the design's frame before anything is compared. Turn it off only for a linear product, where the ends are meaningful." }, "consensus": { "type": "string", "residues": "nt", "description": "The assembled consensus from the sequencing service, raw or FASTA. One record." } }, "additionalProperties": false }arguments 24 linesweb_search unknown never probed
Search the live web (via Tavily) for information not covered by SeqBench's own tools — recent literature, protocols, vendor/reagent info, general facts. Returns a short synthesized answer (if available) plus ranked source snippets with URLs. This does not run any bioinformatics calculation itself; use the dedicated tools for that.
{ "type": "object", "required": [ "query" ], "properties": { "query": { "type": "string", "description": "The search query." }, "max_results": { "type": "number", "description": "Maximum number of results to return (default 5, max 10)." } }, "additionalProperties": false }arguments 17 linesid_map_submit unknown never probed
Submit up to 100,000 ids to UniProt's ID mapping service for a single confirmed-safe hop (e.g. Gene_Name -> UniProtKB-Swiss-Prot, or UniProtKB_AC-ID -> Ensembl/GeneID/RefSeq_Protein/Gene_Name). Returns a jobId immediately — poll it with id_map_poll.
{ "type": "object", "required": [ "ids", "from", "to" ], "properties": { "to": { "type": "string", "description": "Target id type. Supported single hops: Gene_Name/Ensembl/GeneID/RefSeq_Protein -> \"UniProtKB-Swiss-Prot\" (the only direct target for these), or \"UniProtKB_AC-ID\" -> Ensembl/GeneID/RefSeq_Protein/Gene_Name. Any other pair is rejected — chain two of these hops instead." }, "ids": { "type": "array", "items": { "type": "string" }, "description": "The ids to map, up to 100000 (e.g. gene symbols, UniProt accessions, Ensembl gene IDs, Entrez GeneIDs, or RefSeq protein accessions, depending on \"from\")." }, "from": { "type": "string", "description": "Source id type: \"Gene_Name\", \"Ensembl\", \"GeneID\", \"RefSeq_Protein\", or \"UniProtKB_AC-ID\". UniProt's mapping graph is hub-and-spoke — see the \"to\" note." }, "taxId": { "type": "string", "description": "NCBI taxonomy id to disambiguate a gene symbol (only used when from=\"Gene_Name\"). Defaults to human (9606) if omitted." } }, "additionalProperties": false }arguments 30 linesgene_model unknown never probed
The real exon/UTR/CDS structure of a human gene's canonical transcript, fetched live from Ensembl (the same exon/CDS map the HGVS Converter tool uses) — for rendering an exon diagram.
{ "type": "object", "required": [ "gene" ], "properties": { "gene": { "type": "string", "description": "A human gene symbol (\"TP53\") or Ensembl gene ID (\"ENSG00000141510\")." } }, "additionalProperties": false }arguments 13 linesortholog_map unknown never probed
Look up the orthologous (or paralogous) gene for up to 50 gene symbols in a target species, via Ensembl's homology-by-symbol REST endpoint. Symbols with no homology record are reported in `unmapped`, never silently dropped.
{ "type": "object", "required": [ "symbols", "targetSpecies" ], "properties": { "type": { "enum": [ "orthologues", "paralogues", "all" ], "type": "string", "default": "orthologues", "description": "Homology type to return. Defaults to orthologues." }, "symbols": { "type": "array", "items": { "type": "string" }, "description": "Gene symbols to look up, up to 50 (e.g. [\"TP53\", \"BRCA1\"])." }, "sourceSpecies": { "type": "string", "default": "human", "description": "Species the symbols belong to: a common name (human, mouse, rat, zebrafish, fruit_fly, worm, yeast, cow, pig, dog, frog, macaque, chimp) or a scientific name such as \"rattus_norvegicus\". Defaults to \"human\"." }, "targetSpecies": { "type": "string", "description": "Species to find homologs in: a common name (mouse, rat, zebrafish, fruit_fly, worm, yeast, …) or a scientific name such as \"danio_rerio\"." } }, "additionalProperties": false }arguments 36 linesfastq_qc_report unknown never probed
FastQC-style deep quality-control report for a FASTQ file: per-base quality and content, GC and length distributions, sequence duplication levels, overrepresented sequences, and adapter content — each with a warn/fail verdict against FastQC's own published thresholds.
{ "type": "object", "required": [ "input" ], "properties": { "input": { "type": "string", "description": "FASTQ text: records of an '@id' header, sequence, '+' separator and quality line (four lines each)." }, "qualityOffset": { "enum": [ 33, 64 ], "type": "integer", "default": 33, "description": "ASCII offset of the FASTQ quality string. 33 for anything modern, 64 for pre-1.8 Illumina." } }, "additionalProperties": false }arguments 22 linesvolcano_plot_data unknown never probed
Validate a differential-expression table (gene, log2 fold-change, p-value/FDR) and compute -log10(p) plus up/down/non-significant counts at conventional default thresholds (|log2FC|>=1, p<=0.05), for the Volcano Plot visualization. Invalid rows (non-finite log2FC, or p-value outside (0,1]) are dropped and reported rather than failing the whole batch.
{ "type": "object", "required": [ "rows" ], "properties": { "rows": { "type": "array", "items": { "type": "object", "required": [ "gene", "log2fc", "pvalue" ], "properties": { "gene": { "type": "string", "description": "Gene name/id." }, "log2fc": { "type": "number", "description": "log2 fold-change." }, "pvalue": { "type": "number", "description": "p-value, or an adjusted/FDR value — whichever column you want thresholded on. Must be in (0, 1]." } } }, "description": "Differential expression rows, one per gene." } }, "additionalProperties": false }arguments 35 linesexpression_heatmap_cluster unknown never probed
Hierarchically cluster a genes x samples expression matrix (UPGMA/average, complete, or single linkage; Euclidean or correlation distance) and return the row/column leaf order, dendrogram merge trees, and row-z-scored values for the Clustered Expression Heatmap visualization.
{ "type": "object", "required": [ "genes", "samples", "values" ], "properties": { "genes": { "type": "array", "items": { "type": "string" }, "description": "Row (gene) labels." }, "values": { "type": "array", "items": { "type": "array", "items": { "type": "number" } }, "description": "genes x samples numeric matrix — one row per gene, in the same order as `genes`." }, "linkage": { "enum": [ "average", "complete", "single" ], "type": "string", "default": "average", "description": "average = UPGMA (standard default), complete = farthest-neighbor, single = nearest-neighbor." }, "samples": { "type": "array", "items": { "type": "string" }, "description": "Column (sample) labels." }, "zScoreRows": { "type": "boolean", "default": true, "description": "Row-wise z-score each gene's values before clustering and returning (the conventional 'relative expression' heatmap normalization — the dendrograms are computed on the same scaled matrix the heatmap shows, as in seaborn's clustermap(z_score=0) / pheatmap's scale=\"row\")." }, "clusterCols": { "type": "boolean", "default": true, "description": "Cluster (reorder) samples." }, "clusterRows": { "type": "boolean", "default": true, "description": "Cluster (reorder) genes." }, "distanceMetric": { "enum": [ "euclidean", "correlation" ], "type": "string", "default": "correlation", "description": "correlation = 1 - Pearson r (the standard expression-heatmap default); euclidean = straight-line distance." } }, "additionalProperties": false }arguments 69 linesgene_dossier unknown never probed
A gene/drug-target dossier fanned out to five independent sources in one call: Open Targets (function, tractability, top associated diseases), an NCBI/UniProt plain-English function summary, ChEMBL (known drugs and their mechanism/clinical phase, cross-referenced with indications), ClinicalTrials.gov (trials by gene/condition term), and Europe PMC (top cited papers). Each source fails independently — a down source returns null/empty for its own section rather than failing the whole call, and every failure is listed in "sourceErrors" rather than silently omitted.
{ "type": "object", "required": [ "gene" ], "properties": { "gene": { "type": "string", "description": "A human gene symbol (\"TP53\") or Ensembl gene ID (\"ENSG00000141510\")." } }, "additionalProperties": false }arguments 13 linesfunctional_enrichment unknown never probed
Over-representation analysis: test which GO terms (biological process / molecular function / cellular component) and Reactome pathways are statistically enriched in a query gene list versus a background, using the hypergeometric test with Benjamini-Hochberg FDR correction across all tested terms. Uses bundled GO Consortium + Reactome reference data (human only). KEGG is not included (its license does not permit bundling gene sets).
{ "type": "object", "required": [ "genes" ], "properties": { "genes": { "type": "array", "items": { "type": "string" }, "description": "Query gene symbols (human, e.g. \"TP53\"). Case-insensitive. Capped at 5000." }, "background": { "type": "array", "items": { "type": "string" }, "description": "Custom background/universe gene symbols. If omitted, defaults to every gene present in the bundled GO+Reactome dataset (the 'only annotated genes' convention, as used by g:Profiler) rather than the whole genome." }, "collections": { "type": "array", "items": { "enum": [ "GO:BP", "GO:MF", "GO:CC", "Reactome" ], "type": "string" }, "default": [ "GO:BP", "GO:MF", "GO:CC", "Reactome" ], "description": "Which term collections to test. Defaults to all four." }, "maxTermSize": { "type": "integer", "default": 500, "description": "Skip terms/pathways with more than this many background genes (matches clusterProfiler's default)." }, "minTermSize": { "type": "integer", "default": 3, "description": "Skip terms/pathways with fewer than this many background genes." } }, "additionalProperties": false }arguments 52 lineshgvs_convert unknown never probed
Parse an HGVS "c." variant description (by gene symbol, RefSeq NM_, or Ensembl ENST accession), convert it to genomic (g.) coordinates via a real, live-fetched Ensembl exon/CDS map (transcripts resolved through the bundled MANE RefSeq<->Ensembl crosswalk), apply 3'-rule normalization to any del/dup/ins, and predict the protein (p.) effect where that is safely computable. Also accepts a genomic "g." position on a chromosome or RefSeqGene (NC_/NG_, GRCh38 or GRCh37): it is validated and placed on GRCh38 by NCBI, projected onto the MANE Select transcript by Ensembl, and converted back by this tool's own engine, which must agree — so the answer rests on two independent conversions. And the "NC_/NG_(NM_…):c." form converts on the transcript in parentheses. Refuses cleanly — rather than guessing — for circular/mitochondrial genomes, RNA-level or protein-level input, uncertain/mosaic syntax, splice-junction-adjacent or inversion protein effects, and non-MANE/non-Ensembl transcripts.
{ "type": "object", "required": [ "variant" ], "properties": { "variant": { "type": "string", "description": "A full HGVS description: a \"c.\" on a gene symbol or transcript (\"NM_000546.6:c.215C>G\", \"TP53:c.215C>G\"), a \"g.\" position on a chromosome or RefSeqGene (\"NC_000017.11:g.7676154G>C\", \"NG_017013.2:g.16397C>G\"), or a \"c.\" with its transcript in parentheses (\"NC_000017.11(NM_000546.6):c.215C>G\"). Substitution (\">\"), deletion (\"del\"), duplication (\"dup\"), insertion (\"ins\"), delins, and inversion (\"inv\") are supported." } }, "additionalProperties": false }arguments 13 linesbatch unknown never probed
Run one batchable SeqBench tool over many records. Returns a table of per-record results and typed failures.
{ "type": "object", "required": [ "tool", "input" ], "properties": { "args": { "type": "object", "description": "Shared arguments applied to every record.", "additionalProperties": true }, "tool": { "type": "string", "description": "Batchable tool name (for example gc_content or translate)." }, "input": { "type": "string", "description": "Multi-FASTA or one sequence/identifier per line." } }, "additionalProperties": false }arguments 23 linesfastq_trim unknown never probed
Trim FASTQ reads: an ungapped sliding-suffix adapter match (against the same named Illumina adapters as the QC report) followed by a BWA-style 3' quality trim (the same algorithm Cutadapt's own -q option reuses), then drops reads below a minimum length. Returns the trimmed FASTQ plus before/after read-count, mean-length and mean-quality stats.
{ "type": "object", "required": [ "input" ], "properties": { "input": { "type": "string", "description": "FASTQ text: records of an '@id' header, sequence, '+' separator and quality line (four lines each)." }, "minLength": { "type": "integer", "default": 20, "description": "Reads shorter than this after trimming are dropped." }, "qualityOffset": { "enum": [ 33, 64 ], "type": "integer", "default": 33, "description": "ASCII offset of the FASTQ quality string. 33 for anything modern, 64 for pre-1.8 Illumina." }, "qualityThreshold": { "type": "integer", "default": 20, "description": "3' quality-trim threshold (Phred score)." } }, "additionalProperties": false }arguments 32 linesalphafold_lookup unknown never probed
Look up a UniProt accession in the AlphaFold Protein Structure Database (CC-BY 4.0). Returns confidence, model version and structure file URLs, or {found:false} when no prediction exists for that accession.
{ "type": "object", "required": [ "accession" ], "properties": { "accession": { "type": "string", "description": "UniProt accession, e.g. \"P04637\"." } }, "additionalProperties": false }arguments 13 linesgene_expression unknown never probed
A gene's tissue-expression fingerprint: per-tissue median TPM from GTEx (v8) and subcellular localization / RNA tissue-specificity / protein class from the Human Protein Atlas, in one call.
{ "type": "object", "required": [ "gene" ], "properties": { "gene": { "type": "string", "description": "A human gene symbol (\"TP53\") or Ensembl gene ID (\"ENSG00000141510\")." } }, "additionalProperties": false }arguments 13 linesexport_plate_layout unknown never probed
Assign a set of PCR reactions (name + forward/reverse primer + optional template label) to wells on a 96-well plate, row-major (A1, A2, … A12, then B1, B2, … up to H12). Returns the well-assignment data for rendering a plate diagram; export_opentrons_protocol and export_echo_picklist build their downloadable files from this exact same layout, so all three always agree.
{ "type": "object", "required": [ "reactions" ], "properties": { "reactions": { "type": "array", "items": { "type": "object", "required": [ "forward", "reverse" ], "properties": { "name": { "type": "string", "description": "Reaction/construct name." }, "forward": { "type": "string", "description": "Forward primer sequence, 5'->3' (IUPAC accepted)." }, "reverse": { "type": "string", "description": "Reverse primer sequence, 5'->3' (IUPAC accepted)." }, "template": { "type": "string", "description": "Optional template name/id — a short label (e.g. a plasmid or sample name), not a sequence." } } }, "description": "One entry per PCR reaction, up to 96 (a single 96-well plate)." } }, "additionalProperties": false }arguments 38 linesexport_opentrons_protocol unknown never probed
Generate a downloadable Opentrons Python Protocol API (v2, OT-2) script that sets up the given PCR reactions on a 96-well PCR plate, at the same well positions export_plate_layout assigns. Uses real Opentrons labware/pipette API names confirmed against docs.opentrons.com and the Opentrons shared-data labware-definitions repository (opentrons_96_wellplate_200ul_pcr_full_skirt, opentrons_96_tiprack_20ul, opentrons_24_tuberack_nest_1.5ml_snapcap, nest_12_reservoir_15ml, p20_single_gen2) and the confirmed load_labware/load_instrument/transfer method signatures. Master-mix/primer/template/water volumes are clearly-labeled placeholder constants at the top of the script — this is a starting point to review and adapt for your own enzyme and instrument, not a certified ready-to-run protocol.
{ "type": "object", "required": [ "reactions" ], "properties": { "reactions": { "type": "array", "items": { "type": "object", "required": [ "forward", "reverse" ], "properties": { "name": { "type": "string", "description": "Reaction/construct name." }, "forward": { "type": "string", "description": "Forward primer sequence, 5'->3' (IUPAC accepted)." }, "reverse": { "type": "string", "description": "Reverse primer sequence, 5'->3' (IUPAC accepted)." }, "template": { "type": "string", "description": "Optional template name/id — a short label (e.g. a plasmid or sample name), not a sequence." } } }, "description": "One entry per PCR reaction, up to 96 (a single 96-well plate)." }, "protocolName": { "type": "string", "description": "Optional protocol name (used in the script's metadata)." } }, "additionalProperties": false }arguments 42 linesexport_echo_picklist unknown never probed
Generate a downloadable Beckman/Labcyte Echo acoustic-liquid-handler picklist CSV (columns: Source Plate Name, Source Plate Type, Source Well, Destination Plate Name, Destination Well, Transfer Volume, Name — the header row reproduced from PyEcho, a real open-source Echo-picklist generator) for the given PCR reactions, at the same well positions export_plate_layout assigns. Assumes a 5 uL Echo-scale PCR reaction (master mix 2500 nL, each primer 250 nL, template 250 nL, water 1750 nL) — a commonly used acoustic-dispensing miniaturization scale, not a universal standard; rescale the volumes for your own protocol. Source/Destination Plate Type uses a placeholder Echo plate-type code (384PP_AQ_BP) — replace with the exact type from your own Echo Plate Type Library. Each distinct template label gets its own well on the TemplateSource plate, row-major (A1, A2, … A24, then B1, …) across that 384-well source plate.
{ "type": "object", "required": [ "reactions" ], "properties": { "reactions": { "type": "array", "items": { "type": "object", "required": [ "forward", "reverse" ], "properties": { "name": { "type": "string", "description": "Reaction/construct name." }, "forward": { "type": "string", "description": "Forward primer sequence, 5'->3' (IUPAC accepted)." }, "reverse": { "type": "string", "description": "Reverse primer sequence, 5'->3' (IUPAC accepted)." }, "template": { "type": "string", "description": "Optional template name/id — a short label (e.g. a plasmid or sample name), not a sequence." } } }, "description": "One entry per PCR reaction, up to 96 (a single 96-well plate)." } }, "additionalProperties": false }arguments 38 linesvariant_annotate unknown never probed
One-box variant lookup against MyVariant.info: accepts an rsID, chrom:pos:ref:alt (colon- or hyphen-separated), genomic HGVS ("chr17:g.7676154G>C"), or transcript HGVS c. ("NM_000546.6:c.215C>G" / "TP53:c.215C>G", bridged via the hgvs_convert tool). Returns a ClinVar significance summary, gnomAD exome/genome allele frequencies, and CADD/SIFT/PolyPhen2/REVEL pathogenicity predictor scores — each section explicitly null when that source has no data, never silently omitted. See the result's own "caveats" for real data-freshness limits (frozen gnomAD/CADD snapshots, periodic ClinVar snapshot).
{ "type": "object", "required": [ "variant" ], "properties": { "variant": { "type": "string", "description": "An rsID (\"rs1042522\"), chrom:pos:ref:alt with either separator (\"17:7676154:G:C\" or \"17-7676154-G-C\", single-base substitutions only), genomic HGVS (\"chr17:g.7676154G>C\" or \"17:g.7676154G>C\"), or transcript HGVS c. (\"NM_000546.6:c.215C>G\" or \"TP53:c.215C>G\")." }, "assembly": { "enum": [ "hg19", "hg38" ], "type": "string", "default": "hg19", "description": "Genome build for rsID/chrom-pos-ref-alt/genomic-HGVS lookups (MyVariant.info's native default is hg19). Ignored for transcript \"c.\" input, which is always bridged via GRCh38/hg38 (hgvs_convert's own coordinate space)." } }, "additionalProperties": false }arguments 22 linesvariant_to_construct unknown never probed
Turn one variant into one buildable plan: verify the reference allele actually sits where the coordinate says, apply the edit, design site-directed mutagenesis primers to install it, design KASP/ARMS allele-specific primers to genotype it afterwards, and consolidate everything into a single oligo order table. Takes either a construct sequence with a 1-based position and ref/alt alleles (offline, deterministic), or an HGVS "c." description resolved through the MANE crosswalk and a live Ensembl exon map. A mismatched reference allele is refused with the bases that were actually found there, because a coordinate that is right for another isoform yields a perfectly valid primer set for the wrong base. Bases shared by both alleles are trimmed first, so a VCF-anchored pair is designed as the substitution or indel it actually is. Mutagenesis covers every class (a substitution, an insertion, a deletion and a multi-base replacement are all one interval replacement); KASP needs a single-base substitution's 3'-terminal base, so for an indel the genotyping half comes back as a named omission with the reason and the readout that does work, never as an empty list.
{ "type": "object", "required": [], "properties": { "flank": { "type": "integer", "default": 300, "description": "NETWORK MODE. Bases of genomic context fetched either side of the variant (60-1000). Needs to cover the allele-specific core upstream and the genotyping amplicon downstream." }, "label": { "type": "string", "description": "Name stem for the ordered oligos. Defaults to the HGVS string (network mode) or a positional label like \"A100G\" (offline)." }, "style": { "enum": [ "quikchange", "q5" ], "type": "string", "default": "quikchange", "description": "Mutagenic primer style: overlapping (QuikChange) or back-to-back (Q5/KLD)." }, "variant": { "type": "string", "description": "NETWORK MODE. A full HGVS \"c.\" description, e.g. \"NM_000546.6:c.215C>G\" or \"TP53:c.215C>G\". Resolved through the bundled MANE crosswalk and a live Ensembl exon map, then a genomic window is fetched around it. Mutually exclusive with \"sequence\"." }, "position": { "type": "integer", "minimum": 1, "description": "OFFLINE MODE. 1-based position of the first base of refAllele on `sequence`. For a pure insertion (empty refAllele) the alternate bases are inserted immediately BEFORE this position." }, "sequence": { "type": "string", "residues": "nt", "description": "OFFLINE MODE. The reference/construct sequence the variant is described against (raw or FASTA). Mutually exclusive with \"variant\"." }, "altAllele": { "type": "string", "description": "OFFLINE MODE. Bases installed. Use \"-\" or \"\" for a pure deletion." }, "refAllele": { "type": "string", "description": "OFFLINE MODE. Bases replaced, as they appear on `sequence` — checked against it and refused if they differ. Use \"-\" or \"\" for a pure insertion. A VCF-style anchored pair (both alleles carrying a shared flanking base, e.g. refAllele \"T\" / altAllele \"TGGATCC\", or \"TG\" / \"AG\") is accepted and trimmed to its minimal form before anything is designed; the trimmed coordinates are reported as `minimal`." }, "armTmTarget": { "type": "number", "default": 60, "maximum": 80, "minimum": 45, "description": "Target Tm (°C) for each mutagenic primer's template-binding arm (45-80; the arm is grown between 10 and 30 nt, so a target outside that range is refused rather than clamped to the shortest or longest arm)." }, "maxAmplicon": { "type": "integer", "default": 150, "maximum": 10000, "minimum": 36, "description": "Maximum genotyping amplicon length. Refused below 36 bp, the shortest KASP product that can exist (an 18 nt core plus an 18 nt reverse primer), and refused below minAmplicon — both are unsatisfiable for every reference, and left unchecked they came back as \"no common reverse primer could be placed; provide more 3' flanking sequence\"." }, "minAmplicon": { "type": "integer", "default": 60, "maximum": 10000, "minimum": 1, "description": "Minimum genotyping amplicon length, measured from the allele-specific primer's 5' end (which sits one core-length upstream of the variant) to the reverse primer's 5' end. Must not exceed maxAmplicon." }, "targetCoreTm": { "type": "number", "default": 56, "maximum": 80, "minimum": 45, "description": "Target Tm (°C) for the allele-specific genotyping core, before the universal tail (45-80; the core is chosen between 18 and 27 nt, so a target outside that range is refused rather than clamped)." }, "addSecondaryMismatch": { "type": "boolean", "default": true, "description": "Engineer the ARMS destabilizing mismatch 3 nt from the allele-specific primer's 3' end." } }, "additionalProperties": false }arguments 80 linesprime_editing_twin_design unknown never probed
Design a twinPE pegRNA pair (Anzalone et al. 2022) for a replacement too large for a single pegRNA's RTT: a left pegRNA nicks the + strand at/before the replacement window and a right pegRNA nicks the - strand at/after it, each synthesizing a new 3' flap; both flaps are truncated at a shared overlap in the middle of the new sequence so they anneal and resolve the edit without an HDR donor. Coordinates: both pegRNAs' protospacerStart/protospacerEnd/nickPosition are 1-based inclusive in the submitted PRE-EDIT target's frame (the PAM search runs on the unedited sequence, on both sides), while replaceSpan is the span of the new content in the returned editedSequence. Off-target activity is not evaluated (no in-browser reference genome).
{ "type": "object", "required": [ "target", "replaceStart", "replaceEnd", "newSequence" ], "properties": { "target": { "type": "string", "residues": "nt", "description": "Forward-strand target DNA (raw or FASTA), with flanking sequence on both sides of the replacement window." }, "pbsLength": { "type": "integer", "description": "Optional preferred PBS length to highlight; a full 8-17 nt sweep is always returned." }, "replaceEnd": { "type": "integer", "description": "1-based inclusive end of the region being replaced/deleted. For a pure insertion, set replaceEnd = replaceStart - 1." }, "newSequence": { "type": "string", "residues": "nt", "description": "New sequence (forward strand) to install in place of [replaceStart, replaceEnd]. Needs >= 2 bp." }, "replaceStart": { "type": "integer", "description": "1-based inclusive start of the region being replaced/deleted." }, "overlapLength": { "type": "integer", "default": 15, "description": "Length (bp) of the shared overlap built into both pegRNAs' 3' flaps where they meet and anneal." } }, "additionalProperties": false }arguments 39 linesprime_editing_efficiency unknown never probed
Predict per-pegRNA prime-editing efficiency for one edit with PRIDICT2.0, and return the top-scoring pegRNA designs ranked by it. Takes the target as context, the edit in brackets, then context — ACGT...(A/G)...ACGT, with roughly 100+ bp each side — and enumerates PBS/RTT length combinations, scoring every one in HEK293 and K562. Each candidate comes back with both scores, its percentile against the training library, its rank, the spacer, PBS and RTT lengths, the full pegRNA, and Golden Gate cloning oligos. Use it to CHOOSE between designs; the number is not a promised editing percentage. PREDICTED, NOT MEASURED (Spearman ρ = 0.85 on held-out data from the libraries it was trained on). Spearman rho of about 0.85 for intended edits on held-out library data — the best-validated figure of any model in this registry, and roughly double OSTIR's 0.39 on independent data. That figure is still within the library and cell lines it was trained on. Valid for: human sequence, and efficiency ranking within one locus. It is parameterized on HEK293 and K562; your cell type, delivery method, and chromatin context will all move the absolute efficiency, chromatin alone by severalfold. Nothing here is predicted for a non-human host or for editors outside the PE2/PE3 architecture the training libraries used.
{ "type": "object", "required": [ "sequence" ], "properties": { "topN": { "type": "integer", "default": 10, "maximum": 50, "minimum": 1, "description": "How many top-ranked pegRNAs to return, out of the hundreds enumerated. Max 50." }, "cellType": { "enum": [ "HEK", "K562" ], "type": "string", "default": "HEK", "description": "Which trained context to RANK by. Both scores are always returned; this decides the ordering. There is no generic-mammalian option because the model has no such training data." }, "sequence": { "type": "string", "description": "Target with the edit in brackets: context, then (original/edited), then context. Roughly 100+ bp each side — the model reads that context. Keep unchanged flanking bases OUTSIDE the brackets: T(a/g)C, not (TAC/TGC). Insertions and deletions leave one side empty, e.g. (/AGG) or (AGG/)." }, "use5Folds": { "type": "boolean", "default": false, "description": "Average all five trained folds instead of the first. Modestly steadier scores for five times the compute, and it is charged five times as much." } }, "additionalProperties": false }arguments 34 linesbase_editing_design unknown never probed
Design cytosine (CBE, C→T) or adenine (ABE, A→G) base-editing gRNAs for an SpCas9 target: for each NGG gRNA it reports every editable base inside the editor's activity window, flags bystander edits (more than one editable base in the window), and — with a CDS reading frame — classifies each edit's amino-acid consequence (silent / missense / nonsense / stop-loss). Bystander-free guides are ranked first. Handles both strands (a C→T on the protospacer of a reverse-strand guide is reported as the forward-strand G→A).
{ "type": "object", "required": [ "target" ], "properties": { "editor": { "enum": [ "be3", "be4max", "abe7.10", "abe8e" ], "type": "string", "default": "be4max", "description": "Base editor: be3/be4max (CBE, C→T) or abe7.10/abe8e (ABE, A→G)." }, "target": { "type": "string", "residues": "nt", "description": "Nucleotide sequence (raw or FASTA; IUPAC accepted)." }, "frameStart": { "type": "integer", "description": "Optional 1-based CDS reading-frame start, to classify each edit's amino-acid consequence." }, "targetPosition": { "type": "integer", "description": "Optional 1-based forward-strand position of the base you intend to edit; only guides whose window covers it are returned." } }, "additionalProperties": false }arguments 33 linessirna_design unknown never probed
Design siRNA duplexes against an mRNA target using the established Reynolds (2004) 8-criteria score and the Ui-Tei (2004) rules, plus the siDirect seed-duplex Tm off-target flag (≥21.5 °C, computed on siDirect's own RNA/RNA scale: Freier 1986 nearest-neighbor parameters, helix initiation A = −10.8, CT = 100 µM, 100 mM Na⁺). Returns ranked candidates with sense/guide oligos (with UU 3' overhangs) and, per candidate, a ready shRNA cassette (sense–loop–antisense–Pol III terminator). Heuristic sequence rules only — no RNA-folding accessibility model and no transcriptome-wide off-target search. PREDICTED, NOT MEASURED. These are rule counts, not a regression, and no skill statistic is claimed for the ranking. Target-site accessibility is not modeled (no folding) and no transcriptome-wide off-target search is performed, so a top-ranked candidate is a starting point for a knockdown panel, not a predicted knockdown level. Valid for: mRNA targets. The seed Tm is computed on siDirect's own RNA/RNA scale (Freier 1986 parameters, helix initiation A = -10.8, CT = 100 µM, 100 mM Na+) and is not comparable with the DNA/DNA Tm reported elsewhere in the toolkit.
{ "type": "object", "required": [ "target" ], "properties": { "target": { "type": "string", "residues": "nt", "description": "Nucleotide sequence (raw or FASTA; IUPAC accepted)." }, "shRnaLoop": { "type": "string", "default": "TTCAAGAGA", "residues": "nt", "description": "Loop sequence used when assembling the shRNA cassette." }, "minReynolds": { "type": "integer", "default": 6, "description": "Minimum Reynolds score (0–8) to keep; falls back to best-ranked if none qualify." } }, "additionalProperties": false }arguments 25 linesvector_library_search unknown never probed
Browse a curated library of publicly deposited, feature-annotated cloning and expression vectors — by name, category (E. coli cloning/expression, yeast, mammalian, plant binary, BAC/fosmid, recombineering, phage/M13), length window, or annotated feature (e.g. 'T7 promoter', 'ori', 'AmpR'). Each hit reports the vector's accession, length, topology and feature count; vector_library_get returns the sequence and the full feature table. A curated public-record set, NOT a vendor catalog — see the gate's notChecked.
{ "type": "object", "properties": { "limit": { "type": "integer", "default": 25, "maximum": 100, "minimum": 1, "description": "Maximum hits to return. Capped at 100; asking for more is an error, not a silent truncation." }, "query": { "type": "string", "description": "Substring of the vector name or its GenBank definition (case- and punctuation-insensitive, min 2 characters)." }, "feature": { "type": "string", "description": "Substring of an annotated feature's label, type or note (min 2 characters), e.g. \"T7 promoter\", \"kanR\", \"rep_origin\"." }, "category": { "type": "string", "description": "Restrict to one category. An unknown category is an error, not an empty result." }, "maxLength": { "type": "integer", "minimum": 0, "description": "Largest vector length in bp." }, "minLength": { "type": "integer", "minimum": 0, "description": "Smallest vector length in bp." } }, "additionalProperties": false }arguments 35 linesrbs_design unknown never probed
Design a 5' UTR / ribosome binding site for a given CDS. Generates a spread of Shine-Dalgarno cores and SD-to-start spacings, scores every one with OSTIR in the context of your own CDS (which matters — the rate depends on how the RBS interacts with that CDS's 5' folding), and returns them ranked. Supply targetExpression to rank by closeness to a target rate instead of by maximum strength, and supply your existing 5' UTR to get a measured baseline and fold-change for each candidate. Runs ViennaRNA on a shared service and is therefore rate limited (see 429/503). PREDICTED, NOT MEASURED (Spearman ρ = 0.39 on two 5' UTR datasets it was not fitted to). Spearman ρ = 0.39 against measured expression on two 5' UTR datasets it was not fitted to (Gilliot & Gorochowski, Nucleic Acids Res 2024;52(13):e58); reproduced in this repo at ρ = 0.509 on an independent leave-one-context-out split over 194,636 measurements, and at a mean ρ = 0.62 over fifteen further measurement systems it was not fitted to — six species, four reporters, three readouts — on which every learned model tried here scored BELOW it (scripts/rbs-eval) — above the published figure because 65,841 rows of that compilation record no measurement at all (fluorescence mean and s.d. both exactly 0) and are excluded here rather than scored as the weakest expression observed. The widely quoted 53% within 2-fold / 91% within 10-fold are calibration residuals on the fitting set, not held-out validation. Valid for: translation INITIATION only, in E. coli-like Gram-negative hosts (the model is parameterized on the E. coli anti-Shine-Dalgarno sequence). Rankings within one construct context; the absolute value has no units and no meaning.
{ "type": "object", "required": [ "cds" ], "properties": { "cds": { "type": "string", "description": "Coding sequence, raw or FASTA, starting at its start codon. Only the 5' end affects the prediction, so the first ~90 nt is enough. A, C, G, T/U only. Max 10,000 nt." }, "limit": { "type": "number", "default": 10, "description": "How many ranked candidates to return. 1-60." }, "leader": { "type": "string", "description": "Optional 5' context upstream of the designed RBS — the transcribed leader from your promoter. Affects the standby-site term. Defaults to a 20 nt unstructured poly-A leader." }, "currentUtr": { "type": "string", "description": "Optional: your existing 5' UTR (everything upstream of the start codon). Scored as a baseline so each candidate gets a fold-change against it." }, "targetExpression": { "type": "number", "description": "Optional target rate on OSTIR's arbitrary scale. Candidates are then ranked by closeness to it (log-ratio) rather than by maximum strength. Only meaningful against a number produced by this same tool." }, "antiShineDalgarno": { "type": "string", "description": "Optional anti-Shine-Dalgarno sequence (the 16S rRNA 3' end) to model a non-E. coli host. Omit to use OSTIR's own E. coli default." } }, "additionalProperties": false }arguments 34 linesrbs_library_design unknown never probed
Build a ladder of ribosome binding sites whose predicted translation initiation rates are evenly spread, in log space, across a range you choose — the standard way to titrate one enzyme's level in a pathway without guessing. Scores every SD-core/spacing/spacer-composition combination with OSTIR in your own CDS context, then picks one variant per rung. Rungs it cannot fill are reported as GAPS rather than filled with the nearest available variant, so a library that does not really span the range says so. PREDICTED, NOT MEASURED: the ordering comes from a model with ρ ≈ 0.39 against measured expression, which is what makes it usable for ranking a library you will screen and unusable for hitting an absolute number. PREDICTED, NOT MEASURED (Spearman ρ = 0.39 on two 5' UTR datasets it was not fitted to). Spearman ρ = 0.39 against measured expression on two 5' UTR datasets it was not fitted to (Gilliot & Gorochowski, Nucleic Acids Res 2024;52(13):e58); reproduced in this repo at ρ = 0.509 on an independent leave-one-context-out split over 194,636 measurements, and at a mean ρ = 0.62 over fifteen further measurement systems it was not fitted to — six species, four reporters, three readouts — on which every learned model tried here scored BELOW it (scripts/rbs-eval) — above the published figure because 65,841 rows of that compilation record no measurement at all (fluorescence mean and s.d. both exactly 0) and are excluded here rather than scored as the weakest expression observed. The widely quoted 53% within 2-fold / 91% within 10-fold are calibration residuals on the fitting set, not held-out validation. Valid for: translation INITIATION only, in E. coli-like Gram-negative hosts (the model is parameterized on the E. coli anti-Shine-Dalgarno sequence). Rankings within one construct context; the absolute value has no units and no meaning.
{ "type": "object", "required": [ "cds" ], "properties": { "cds": { "type": "string", "residues": "nt", "description": "The coding sequence, raw or FASTA, starting at its start codon. Only the 5' end affects the prediction, so the first ~90 nt is enough. Max 10,000 nt." }, "leader": { "type": "string", "description": "Sequence upstream of the RBS (the 5' end of the transcript). OSTIR needs some 5' context for its standby-site term; a 20 nt A-rich leader is assumed when none is given, which is an assumption and not a measurement." }, "targetMax": { "type": "number", "description": "Strongest rung, in the same arbitrary units. Omit with targetMin to use the candidates' own range." }, "targetMin": { "type": "number", "description": "Weakest rung, in OSTIR's arbitrary units. OMIT THIS and the range is taken from what the candidates actually reach in your CDS context, which is usually what you want: the units have no absolute meaning, so a number carried over from a paper or a default describes nothing. Set it only when you are matching a value you measured yourself in the same context." }, "librarySize": { "type": "integer", "default": 8, "maximum": 24, "minimum": 2, "description": "How many variants the ladder should have (default 8)." }, "antiShineDalgarno": { "type": "string", "description": "Override the host's anti-Shine-Dalgarno sequence. Defaults to the E. coli one OSTIR is parameterised on." } }, "additionalProperties": false }arguments 37 linesworkflow unknown never probed
Run an ordered multi-tool pipeline over many records. One sequence value can be chained between steps.
{ "type": "object", "required": [ "steps", "input" ], "properties": { "input": { "type": "string", "description": "Multi-FASTA or one sequence/identifier per line." }, "steps": { "type": "array", "items": { "type": "object", "required": [ "tool" ], "properties": { "args": { "type": "object", "additionalProperties": true }, "from": { "description": "Sequence source: \"initial\" or an earlier step index (0-based)." }, "tool": { "type": "string" } }, "additionalProperties": false }, "maxItems": 8, "minItems": 1 } }, "additionalProperties": false }arguments 38 linesrbs_occlusion unknown never probed
Find every stretch of a transcript that is reverse-complementary to the ribosome's footprint (-20 to +13 around the start codon), with the length and nearest-neighbour Tm of each duplex, and flag the ones that cover the Shine-Dalgarno core or the start codon. This is the mechanism every translational switch runs on — riboswitch, toehold switch, RNA thermometer, antisense repressor — and the first thing to look at when a switch does not switch or a construct is unexpectedly silent. Also reports where a sensor domain can be inserted without touching the site. Deterministic base-pairing, not a folding prediction: use rna_fold to ask whether a given stem actually wins at 37 °C. Reports no switching ratio — see this tool's notes for why.
{ "type": "object", "required": [ "sequence" ], "properties": { "maxLoop": { "type": "integer", "default": 100, "minimum": 3, "description": "Largest number of unpaired bases allowed between an arm and its target (default 100)." }, "minStem": { "type": "integer", "default": 6, "maximum": 40, "minimum": 4, "description": "Shortest duplex to report, in bp (default 6). Below 4 bp every sequence pairs with everything; a stem that actually holds a site shut is usually 8 bp or more." }, "sequence": { "type": "string", "residues": "nt", "description": "The transcript: the 5' UTR plus at least the start of the CDS. DNA or RNA. Max 20,000 nt." }, "startCodonAt": { "type": "integer", "description": "1-based position of the start codon to anchor the footprint on. Omit to use the first ATG/GTG/TTG — pass it when the transcript has several, which is the usual case for a real 5' UTR." } }, "additionalProperties": false }arguments 31 linesriboswitch_states unknown never probed
Fold a transcript twice — once freely, once with the aptamer held out of the secondary structure as a bound ligand would hold it — and report what changes at the ribosome binding site. Returns both structures, both free energies, the cost of occupying the aptamer, and whether the site becomes more or less accessible. This is the question a riboswitch design can be checked on before the bench: is the site sequestered in one state and free in the other. Returns NO activation ratio and no fold-change — see this tool's validation note for why that number is not offered. Pair with rbs_occlusion, which finds what can pair over the site in the first place. PREDICTED, NOT MEASURED. None is published for this combination, and none is claimed. The two folds are ViennaRNA MFE structures with its documented parameter set; what is NOT established is that the ligand-bound state is modelled correctly by holding the aptamer out of the secondary structure, which is an approximation of a three-dimensional binding event. No activation ratio is returned, because the only published validation set for predicting one (Espah Borujeni et al., NAR 2016;44(1):1) is CC BY-NC and unusable here. Valid for: single-strand RNA up to 1,000 nt at one temperature, with no pseudoknots and no tertiary structure. A translational riboswitch whose mechanism is sequestering the ribosome binding site — NOT transcriptional attenuators, NOT ribozymes, and NOT any switch whose aptamer overlaps the site it regulates.
{ "type": "object", "required": [ "sequence" ], "properties": { "siteEnd": { "type": "integer", "description": "1-based end of that region." }, "sequence": { "type": "string", "residues": "nt", "description": "The transcript: aptamer, expression platform, and at least the start of the CDS. DNA or RNA. Max 1,000 nt, because it is folded twice." }, "siteStart": { "type": "integer", "description": "1-based start of the region whose accessibility is the answer. Omit both ends and the ribosome footprint is located automatically from the first start codon and its Shine-Dalgarno." }, "aptamerEnd": { "type": "integer", "description": "1-based end of the aptamer." }, "temperature": { "type": "number", "default": 37, "maximum": 120, "minimum": -20, "description": "Folding temperature in °C. A switch characterised at 37 °C is not a switch at 30 °C." }, "aptamerStart": { "type": "integer", "description": "1-based start of the aptamer — the region the ligand occupies. Omit both ends to fold freely and only report the site's accessibility." } }, "additionalProperties": false }arguments 37 linesvector_library_get unknown never probed
Return one vector from the library: its GenBank accession and version, length, topology, organism/definition, complete sequence, and the full annotated feature table (type, label, 1-based inclusive start/end, strand, spliced length, and the location descriptor as the record wrote it). Accepts the library id, the vector name, or the accession. An unrecognized id is an error carrying the closest names — never an empty result.
{ "type": "object", "required": [ "id" ], "properties": { "id": { "type": "string", "description": "Library id (e.g. \"pbr322\"), vector name (\"pBR322\"), or accession (\"J01749\" / \"J01749.1\")." }, "includeSequence": { "type": "boolean", "default": true, "description": "Set false for the annotation only — useful for a large BAC where the bases are not the point." } }, "additionalProperties": false }arguments 18 linesparts_library_search unknown never probed
Search a parts list harvested from the annotated features of the vector library — promoters, terminators, RBSs, polyA signals, origins, selection markers, affinity tags, reporters, linkers/MCSs — by name, kind or length. Nothing here is transcribed: every part is the exact sequence a GenBank record annotated, and each hit carries the accession and 1-based span it was cut from, plus every other library vector the same part was found in. Parts whose location is spliced or approximate are excluded, because their sequence is not fully determined.
{ "type": "object", "properties": { "kinds": { "type": "array", "items": { "type": "string" }, "description": "Restrict to these part kinds (promoter, terminator, origin, RBS, polyA, selection marker, affinity tag, reporter, linker/MCS, …). An unknown kind is an error." }, "limit": { "type": "integer", "default": 25, "maximum": 100, "minimum": 1, "description": "Maximum hits to return. Capped at 100; asking for more is an error, not a silent truncation." }, "query": { "type": "string", "description": "Substring of the part name (min 2 characters), e.g. \"T7\", \"AmpR\", \"SV40 polyA\"." }, "maxLength": { "type": "integer", "minimum": 0, "description": "Largest part length in bp." }, "minLength": { "type": "integer", "minimum": 0, "description": "Smallest part length in bp." }, "includeSequence": { "type": "boolean", "default": true, "description": "Include each part's bases (5'→3' on the part's own strand)." } }, "additionalProperties": false }arguments 39 lines
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