Reverse, complement and reverse complement of a DNA or RNA sequence.

Parameter	Type	Required	Notes
sequence	string	yes	Nucleotide sequence (raw or FASTA; IUPAC accepted).
type	string	no	—

GC content, AT content and per-base composition of a sequence.

Parameter	Type	Required	Notes
sequence	string	yes	Nucleotide sequence (raw or FASTA; IUPAC accepted).

Translate a nucleotide sequence to protein (single frame or all six frames; standard code).

Parameter	Type	Required	Notes
sequence	string	yes	Nucleotide sequence (raw or FASTA; IUPAC accepted).
frame	integer	no	—
toStop	boolean	no	Stop at the first stop codon.

Find open reading frames (ATG…stop) across all six frames.

Parameter	Type	Required	Notes
sequence	string	yes	Nucleotide sequence (raw or FASTA; IUPAC accepted).
minAaLength	integer	no	Minimum protein length (aa) to report.
requireStop	boolean	no	Only report ORFs terminated by a stop codon.

Clean, case-fold, DNA↔RNA convert, reverse and line-wrap a sequence.

Parameter	Type	Required	Notes
sequence	string	yes	Nucleotide sequence (raw or FASTA; IUPAC accepted).
stripNonLetters	boolean	no	Remove digits, spaces and gaps (keep letters only).
caseMode	string	no	—
convert	string	no	DNA→RNA (T→U) or RNA→DNA (U→T).
reverse	boolean	no	Reverse the sequence (no complement).
width	integer	no	Line-wrap width; 0 = single line.

Find (overlapping) occurrences of an IUPAC motif on either strand, allowing mismatches.

Parameter	Type	Required	Notes
sequence	string	yes	Nucleotide sequence (raw or FASTA; IUPAC accepted).
motif	string	yes	Query motif; IUPAC ambiguity codes (R Y S W K M B D H V N) allowed.
searchReverseStrand	boolean	no	Also search the reverse strand.
maxMismatches	integer	no	Maximum allowed mismatches per match.

Back-translate a protein to DNA (most-frequent codon per organism, or degenerate IUPAC consensus).

Parameter	Type	Required	Notes
protein	string	yes	Protein sequence (one-letter codes; * for stop).
mode	string	no	—
organism	string	no	Codon-usage host (ignored in degenerate mode).

Generate a random DNA, RNA or protein sequence, optionally with a target GC content.

Parameter	Type	Required	Notes
kind	string	no	—
length	integer	yes	Number of residues to generate.
gcContent	number	no	Target GC percentage 0..100 (dna/rna only); omit for uniform.

Primer/oligo melting temperature: nearest-neighbour (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.

Parameter	Type	Required	Notes
sequence	string	yes	Nucleotide sequence (raw or FASTA; IUPAC accepted).
oligoNM	number	no	Total strand concentration (nM).
naMM	number	no	Monovalent cation [Na+]/[K+] (mM).
mgMM	number	no	Divalent cation [Mg2+] (mM).
dntpMM	number	no	Total [dNTP] (mM), chelates Mg2+.
targetTm	number	no	Optional target Tm (°C). When given, the response includes a pass/fail gate.
tmTolerance	number	no	Allowed +/- window (°C) around targetTm for the gate.

Full oligo analysis: nearest-neighbour Tm/ΔG/ΔH/ΔS plus hairpin and self-dimer screening with base-pair diagrams and warnings.

Parameter	Type	Required	Notes
sequence	string	yes	Nucleotide sequence (raw or FASTA; IUPAC accepted).
oligoNM	number	no	Total strand concentration (nM).
naMM	number	no	Monovalent cation [Na+]/[K+] (mM).
mgMM	number	no	Divalent cation [Mg2+] (mM).
dntpMM	number	no	Total [dNTP] (mM), chelates Mg2+.

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 ta

Parameter	Type	Required	Notes
template	string	yes	Nucleotide sequence (raw or FASTA; IUPAC accepted).
forwardPrimer	string	no	Primer 1, 5'→3'.
reversePrimer	string	no	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 e
maxMismatches	integer	no	Mismatches tolerated per primer (0–10).
maxProductLength	integer	no	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 — mak
circular	boolean	no	Treat the template as circular (plasmid).

De-novo PCR primer design (Primer3-style penalty picker): enumerate and score candidate primer pairs against length/Tm/GC/3'-clamp/structure constraints.

Parameter	Type	Required	Notes
template	string	yes	Nucleotide sequence (raw or FASTA; IUPAC accepted).
lenMin	integer	no	—
lenOpt	integer	no	—
lenMax	integer	no	—
tmMin	number	no	—
tmOpt	number	no	—
tmMax	number	no	—
tmMaxDiff	number	no	Max Tm difference within a pair (°C).
gcMin	number	no	—
gcMax	number	no	—
ampliconMin	integer	no	—
ampliconMax	integer	no	—
targetStart	integer	no	1-based inclusive start of a region the product must span (optional).
targetEnd	integer	no	1-based inclusive end of the target region (optional).
maxReturn	integer	no	Number of best pairs to return.
oligoNM	number	no	Total strand concentration (nM).
naMM	number	no	Monovalent cation [Na+]/[K+] (mM).
mgMM	number	no	Divalent cation [Mg2+] (mM).
dntpMM	number	no	Total [dNTP] (mM), chelates Mg2+.

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.

Parameter	Type	Required	Notes
type	string	no	Molecule type.
length	integer	no	Length in bp (dsDNA) or nt (ssDNA/ssRNA). Ignored when a sequence is given.
massNg	number	no	Mass in nanograms.
volumeUl	number	no	Volume in microlitres (0 = unknown; needed for concentration).
sequence	string	no	Optional sequence — overrides length and gives an exact molar mass from base composition.
targetConcentration	number	no	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
targetUnit	string	no	Unit for targetConcentration.
targetVolumeUl	number	no	Final volume of the diluted sample, in µL.

Design site-directed mutagenesis primers (QuikChange overlapping or Q5 back-to-back) for a nucleotide substitution or an amino-acid codon swap.

Parameter	Type	Required	Notes
template	string	yes	Nucleotide sequence (raw or FASTA; IUPAC accepted).
mutation	string	no	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
editKind	string	no	Edit level. Normally omitted — it is inferred from the fields you send (newBase means nt, targetAa means aa, insert/deleteLength means delins).
style	string	no	Mutagenic primer style.
armTmTarget	number	no	Target Tm (°C) for each template-binding arm.
position	integer	no	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
newBase	string	no	Replacement base (nt edit).
deleteLength	integer	no	Template bases to remove, starting at position (delins edit). 0 with insert set is a pure insertion, placed immediately before position.
insert	string	no	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
frameStart	integer	no	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.
residue	integer	no	1-based residue number to change (aa edit).
targetAa	string	no	Target amino acid, one-letter code incl '*' (aa edit).
organism	string	no	Codon-usage table for choosing the new codon (aa edit). Latin names and common strain/cell-line names are accepted.
oligoNM	number	no	Total strand concentration (nM).
naMM	number	no	Monovalent cation [Na+]/[K+] (mM).
mgMM	number	no	Divalent cation [Mg2+] (mM).
dntpMM	number	no	Total [dNTP] (mM), chelates Mg2+.

Screen two oligos for the most stable heterodimer (cross-dimer) between them.

Parameter	Type	Required	Notes
sequenceA	string	yes	First oligo (5'→3').
sequenceB	string	yes	Second oligo (5'→3').

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 pl

Parameter	Type	Required	Notes
forwardPrimer	string	yes	Forward primer, 5'→3'.
reversePrimer	string	yes	Reverse primer, 5'→3'.
maxMismatches	integer	no	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 shorte
maxProductLength	integer	no	Ignore candidate off-target products longer than this (bp) — a search-window cap, not a biological claim.
intendedTemplate	string	no	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 m

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 prim

Parameter	Type	Required	Notes
a	string	yes	First oligo, 5'→3'. Max 200 nt.
b	string	no	Second oligo. Omit to analyse hairpin structure in 'a' alone; pass the same sequence as 'a' for a homodimer.
alphabet	string	no	Which measured parameter set to use. This is not cosmetic — the same 20-mer can differ by several kcal/mol between them.
temperature	number	no	°C. Primer dimers matter at the annealing temperature, not at 37 °C.
partition	boolean	no	Also compute the ensemble free energy over all structures, not just the MFE one. Costs a second pass.

Find restriction enzyme recognition sites in a DNA sequence.

Parameter	Type	Required	Notes
sequence	string	yes	Nucleotide sequence (raw or FASTA; IUPAC accepted).
enzymes	array	no	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
circular	boolean	no	Treat the sequence as circular (plasmid) so sites spanning the origin are found.

Recommend a single NEB buffer (and flag caveats) for digesting with two enzymes in one tube.

Parameter	Type	Required	Notes
enzymeA	string	yes	First enzyme name (e.g. EcoRI).
enzymeB	string	yes	Second enzyme name (e.g. BamHI).

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 modelled as its own chemistry rather than as one product model with different labels: LIC's chew-back stops at the first

Parameter	Type	Required	Notes
method	string	yes	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 (sequenc
fragments	array	no	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
names	array	no	Optional labels for each fragment.
circular	boolean	no	Produce a circular product.
overlapLen	integer	no	Gibson homology-arm length (bp).
mergePreAddedArms	boolean	no	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
armTmTarget	number	no	Target annealing Tm (°C) for primer arms.
enzyme	string	no	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.
vector	string	no	Vector sequence (restriction, topo and lic methods; for lic, the LINEARISED vector).
insert	string	no	Insert sequence (restriction, topo and lic methods).
enzyme5	string	no	Insert 5′ enzyme (restriction method).
enzyme3	string	no	Insert 3′ enzyme (restriction method).
vectorEnzyme5	string	no	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.
vectorEnzyme3	string	no	Vector 3′ enzyme (restriction method); defaults to enzyme3.
dephosphorylateVector	boolean	no	CIP/rSAP-dephosphorylate the vector to suppress self-ligation background (restriction method).
topoMode	string	no	TOPO chemistry (topo method): TA (Taq 3′-A), blunt, or directional (pENTR/D-TOPO, needs 5′-CACC on the insert).
vectorNucleotide	string	no	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 n
insertNucleotide	string	no	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,
chewBackLen	integer	no	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
homologyLen	integer	no	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

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.

Parameter	Type	Required	Notes
sequence	string	yes	Nucleotide sequence (raw or FASTA; IUPAC accepted).

Lint a coding DNA sequence for premature stops, internal RBS/polyA motifs, unwanted restriction sites, GC extremes and repeats.

Parameter	Type	Required	Notes
sequence	string	yes	Nucleotide sequence (raw or FASTA; IUPAC accepted).
frameStart	integer	no	1-based nucleotide where the reading frame begins.
avoidEnzymes	array	no	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 unrecognised name is re
gcWindow	integer	no	Sliding-window size (nt) for GC-extreme scanning.
gcLow	number	no	GC% below this flags an AT-rich window.
gcHigh	number	no	GC% above this flags a GC-rich window.
homopolymerMin	integer	no	Minimum run length to flag a homopolymer.
crypticOrfMinAa	integer	no	Minimum peptide length (aa) for a hidden alternate-frame ORF to be flagged.

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 nat

Parameter	Type	Required	Notes
sequence	string	yes	Nucleotide sequence (raw or FASTA; IUPAC accepted).
organism	string	no	Codon-usage table to prefer among synonymous options.
frameStart	integer	no	1-based nucleotide where the reading frame begins.
avoidEnzymes	array	no	Enzyme names whose internal sites should be removed (e.g. ["BsaI","BsmBI"] for Golden Gate domestication).
gcWindow	integer	no	—
gcLow	number	no	—
gcHigh	number	no	—
homopolymerMin	integer	no	—
crypticOrfMinAa	integer	no	Minimum peptide length (aa) for a hidden alternate-frame ORF to be flagged.
maxPasses	integer	no	Repeat full passes until clean or no further progress.

Predict restriction-digest fragment sizes and their gel migration positions against a chosen DNA ladder.

Parameter	Type	Required	Notes
sequence	string	yes	Nucleotide sequence (raw or FASTA; IUPAC accepted).
enzymes	array	no	Enzyme names to digest with, from the curated common-enzyme set (see restriction_sites for the full list). An unrecognised name is rejected rather than skipped, so an empty band pattern always means "
circular	boolean	no	Treat the sequence as circular (plasmid).
ladder	string	no	DNA ladder to plot alongside the sample lane.

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

Parameter	Type	Required	Notes
vectorLengthBp	integer	yes	Backbone length in bp.
vectorNgPerUl	number	yes	Backbone stock concentration, ng/µL.
vectorNg	number	no	How much backbone to put in the reaction, ng. This is the quantity you fix; every insert mass follows from the ratio.
insertLengthBp	integer	no	Insert length in bp. Use inserts instead for a multi-fragment assembly.
insertNgPerUl	number	no	Insert stock concentration, ng/µL.
molarRatio	number	no	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.
inserts	array	no	Multi-fragment assembly: one entry per insert, each with its own length, stock and molar equivalents. Overrides insertLengthBp/insertNgPerUl/molarRatio when present.
reactionVolumeUl	number	no	Total reaction volume, µL.
vectorSequence	string	no	Optional backbone sequence — gives an exact molar mass from base composition instead of the 650 g/mol/bp average.

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 si

Parameter	Type	Required	Notes
parts	array	yes	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 m
enzyme	string	no	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 overhan

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-circularised — 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

Parameter	Type	Required	Notes
fragments	array	yes	The parts in assembly order, raw or FASTA — the same list cloning_simulate takes. 2-8 parts.
names	array	no	Optional labels for the parts, in the same order ("backbone", "promoter", "CDS"). Used in every outcome label.
method	string	no	How the parts are joined. Golden Gate junctions are the Type IIS fusion overhangs; Gibson junctions are the homology arms.
enzyme	string	no	Golden Gate only — the Type IIS enzyme, which fixes the overhang length (BsaI, BbsI, Esp3I (BsmBI)).
overlapLen	number	no	Gibson only — homology arm length, which must match what the assembly was designed with.
dataset	string	no	Which ligation dataset to read overhang cross-talk from (Golden Gate only).
circular	boolean	no	Circular product. Only circular assemblies are covered — a linear product's leading end is a free terminus, not a junction.
maxAlternatives	number	no	Cap on returned alternatives, most accessible first. The pre-cap count is always reported as alternativesEnumerated.

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

Parameter	Type	Required	Notes
intended	string	yes	The construct you designed, raw or FASTA.
alternatives	array	yes	The wrong constructs to screen against, 1-12. assembly_outcomes emits these ready-made as forDiagnosticDigest.
circular	boolean	no	Treat every candidate as a circular plasmid.
agarosePercent	number	no	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 sep
enzymes	array	no	Restrict the search to these enzymes (e.g. the ones on your bench). Default is the whole curated set of 49. An unrecognised name is rejected rather than skipped, so "does not discriminate" always mean
includePairs	string	no	Whether to search double digests. "auto" adds them only when no single enzyme separates everything.
maxSuggestions	number	no	How many ranked options to return.

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 le

Parameter	Type	Required	Notes
sequence	string	yes	The construct, raw or FASTA. Max 500,000 bp.
circular	boolean	no	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.
minRepeatLength	number	no	Shortest repeat to report, in bp (default 20). Below about 20 bp homologous recombination has little to work with and chance matches multiply.
maxPairs	number	no	Cap on reported pairs, most recombinogenic first. The pre-cap count is always reported as pairsFound.
includeSequences	boolean	no	Return the full product sequences. Turn off for a coordinates-only summary over a large construct.

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 assign

Parameter	Type	Required	Notes
template	string	yes	The template you amplified, raw or FASTA. Max 200,000 bp.
forwardPrimer	string	yes	Forward primer, 5'→3'.
reversePrimer	string	yes	Reverse primer, 5'→3'.
observedSize	number	yes	The band size you measured off the gel, in bp.
tolerancePercent	number	no	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.
toleranceBp	number	no	Override the tolerance with a fixed window in bp.
circular	boolean	no	Template is circular (a plasmid).
maxMismatches	number	no	Mismatches tolerated per primer while looking for sites (max 6). Higher finds more explanations and more coincidences.
maxCandidates	number	no	Cap on returned candidates, best-anchored first.

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 le

Parameter	Type	Required	Notes
controlBases	string	yes	Base calls of the UNEDITED control read.
controlChannels	array	yes	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).
editedBases	string	yes	Base calls of the edited pool's read.
editedChannels	array	yes	Per-base [A, C, G, T] intensities of the edited read, same convention.
cutPosition	number	yes	1-based position of the expected cut, in CONTROL read coordinates.
maxIndel	number	no	Largest indel to include in the basis, in bp (max 20). Every shift from −maxIndel to +maxIndel is fitted.
windowLength	number	no	Bases downstream of the cut used for the decomposition (20-300). Longer is better conditioned but needs more clean read.
guard	number	no	Bases skipped immediately after the cut, where the trace is least reliable.
offset	number	no	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.

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

Parameter	Type	Required	Notes
targets	array	yes	2-8 targets to amplify in one reaction.
agarosePercent	number	no	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, whi
dimerThresholdDG	number	no	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.
internalDimerThresholdDG	number	no	The looser bar for a cross-dimer that pairs internally and only sequesters primer.
maxTmSpread	number	no	Widest Tm difference tolerated across every primer in the panel, in °C — one annealing temperature has to serve all of them.
candidatesPerTarget	number	no	Candidate pairs considered per target (max 6). More finds a panel where fewer cannot, at the cost of a larger search.
ampliconMin	number	no	Panel-wide default product size floor, for targets that set none.
ampliconMax	number	no	Panel-wide default product size ceiling.

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 t

Parameter	Type	Required	Notes
symptom	string	yes	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 ban
method	string	yes	How the construct was made. Decides which cause set applies and which design checks can run.
parts	array	no	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.
partNames	array	no	Labels for the parts, in the same order ("backbone", "promoter", "CDS"). Used in every fact that names a part.
enzymes	array	no	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 unrecognised name is rejected rather than skipped: every
overlapLen	number	no	Gibson only — the homology arm length the assembly was designed with.
template	string	no	PCR template, raw or FASTA.
templateCircular	boolean	no	Treat the template as a plasmid, so a product across the origin is found.
primerForward	string	no	Forward primer, up to 200 nt.
primerReverse	string	no	Reverse primer, up to 200 nt.
annealingTempC	number	no	Annealing temperature actually used, °C. Compared against each primer's own nearest-neighbour Tm.
agarosePercent	number	no	Agarose percentage of the gel. Snapped to the nearest tabulated value; decides the resolving window a band is placed against.
hostMethylation	string	no	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
phosphataseTreated	boolean	no	Was the cut vector dephosphorylated (rSAP/CIP) before ligation?
insertSource	string	no	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	string	no	Selection marker on the vector. Compared against the plate's antibiotic by identity, not by guessing at free text.
plateAntibiotic	string	no	Antibiotic on the plate. amp and carbenicillin count as the same selection (both select bla).
colonies	number	no	Colonies on the experimental plate. Omitting this is different from giving 0.
noDnaControlColonies	number	no	Colonies from the same cells and plate with NO DNA added. Non-zero means the plate is not selecting.
positiveControlColonies	number	no	Colonies from an intact, uncut plasmid into the same cell aliquot. Non-zero eliminates "the cells never took up DNA".

Protein properties: molecular weight, isoelectric point, GRAVY, extinction coefficient and composition.

Parameter	Type	Required	Notes
sequence	string	yes	Protein sequence (one-letter amino-acid codes; non-AA characters ignored).
chargeStep	number	no	pH step along the net-charge titration curve, which always spans pH 0-14. Between 0.001 and 14.

Sliding-window hydropathy/hydrophobicity profile (ProtScale-style) over a published amino-acid scale.

Parameter	Type	Required	Notes
sequence	string	yes	Protein sequence (one-letter amino-acid codes; non-AA characters ignored).
scale	string	no	Amino-acid scale. Kyte-Doolittle and Eisenberg are hydrophobicity; Hopp-Woods is hydrophilicity.
window	integer	no	Sliding-window size (clamped to an odd number ≥ 1).

In-silico protease/chemical digestion: cleave a protein and report each peptide's position, length and neutral mass.

Parameter	Type	Required	Notes
sequence	string	yes	Protein sequence (one-letter amino-acid codes; non-AA characters ignored).
protease	string	no	Protease or chemical cleavage agent.
missedCleavages	integer	no	Allowed missed internal cleavages (0–2).
minMass	number	no	Optional lower bound on neutral monoisotopic mass (Da).
maxMass	number	no	Optional upper bound on neutral monoisotopic mass (Da).
maxPeptides	integer	no	Cap on the number of returned peptides.

Codon-optimise a protein (or coding DNA) for an expression host by picking the most-frequent codon per residue.

Parameter	Type	Required	Notes
protein	string	yes	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 optimised).
organism	string	no	—
inputType	string	no	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.

Codon Adaptation Index (CAI) and per-codon relative adaptiveness of a CDS against an expression host, with rare-codon and GC3 analysis.

Parameter	Type	Required	Notes
sequence	string	yes	Coding sequence (DNA/RNA; should start in-frame at ATG).
organism	string	no	—
frameStart	integer	no	1-based position to start reading codons.
rareThreshold	number	no	Relative adaptiveness (w) below this flags a codon as rare.

Global (Needleman-Wunsch), local (Smith-Waterman) or semi-global/fitting pairwise alignment of two sequences, with match/mismatch scoring and affine gap costs (Gotoh).

Parameter	Type	Required	Notes
seqA	string	yes	First sequence (raw or FASTA; nucleotide or protein).
seqB	string	yes	Second sequence (raw or FASTA; nucleotide or protein).
mode	string	no	"global" penalises 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
match	number	no	Match score.
mismatch	number	no	Mismatch penalty.
gap	number	no	Affine gap EXTEND penalty, charged per gap position (including the first).
gapOpen	number	no	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

Center-star multiple sequence alignment of a multi-FASTA input, with consensus and per-column conservation.

Parameter	Type	Required	Notes
input	string	yes	Two or more sequences in multi-FASTA format (>name / sequence). Up to 25 are aligned.

Align a query to a reference and call variants (substitutions, insertions, deletions) in HGVS g. notation, with optional coding effects.

Parameter	Type	Required	Notes
reference	string	yes	Reference / wild-type sequence (raw or FASTA).
query	string	yes	Query / variant sequence (raw or FASTA).
coding	boolean	no	Treat as a coding sequence and report amino-acid effects.
frameStart	integer	no	1-based reading-frame start (used when coding is true).

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

Parameter	Type	Required	Notes
reference	string	yes	The intended construct (raw or FASTA). Up to 20,000 bp.
reads	string	yes	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
circular	boolean	no	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.
insertStart	integer	no	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 plasm
insertEnd	integer	no	1-based last base of that stretch.
insertLabel	string	no	What to call it in the verdicts. Default "the insert".
grouping	string	no	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.
trimThreshold	integer	no	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.
qualityOffset	integer	no	ASCII offset of the FASTQ quality string. 33 for anything modern, 64 for pre-1.8 Illumina.

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 in accuracy by Rule Set 2 / Azimuth and by DeepSpCas9, neither of which is shipped here. Treat the ordering as a ranking aid, not an efficiency prediction. Valid for: Sp

Parameter	Type	Required	Notes
sequence	string	yes	Nucleotide sequence (raw or FASTA; IUPAC accepted).
nuclease	string	no	Nuclease id. Omit to just list the available nucleases (no scan is performed).
searchReverseStrand	boolean	no	Also scan the reverse strand for guides.
minScore	number	no	Only return guides with a heuristic score at least this high (0–100).

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

Parameter	Type	Required	Notes
protospacer	string	yes	The guide's protospacer sequence, 5'→3' (no PAM). Max 32 nt — every supported nuclease uses a 20–23 nt guide.
nuclease	string	no	Nuclease id — determines the PAM pattern/side required at each candidate site.
maxMismatches	integer	no	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 selec

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

Parameter	Type	Required	Notes
targetSequence	string	yes	Nucleotide sequence (raw or FASTA; IUPAC accepted).
editStart	integer	no	1-based start of the region being replaced. Omit to derive from guideStart/guideEnd/guideStrand instead.
editEnd	integer	no	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.
guideStart	integer	no	1-based forward-strand start of the guide's protospacer (alternative to editStart/editEnd, for an insertion exactly at the cut site).
guideEnd	integer	no	1-based forward-strand end of the guide's protospacer.
guideStrand	string	no	Strand the guide's protospacer is on.
nuclease	string	no	Needed only when deriving the cut site from guideStart/guideEnd/guideStrand.
replacement	string	yes	Sequence to insert/substitute ("" for a pure deletion).
armLength	integer	no	Homology arm length (bp) on each side. Use ~30–60 for an ssODN donor, ~500–1000 for a dsDNA donor plasmid.
designGenotypingPrimers	boolean	no	Also design a primer pair (on the original targetSequence) whose product spans the edit site.
blockPam	boolean	no	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-cu
frameStart	integer	no	Optional 1-based CDS reading-frame start; makes the PAM-blocking mutation synonymous where possible.

Parse a GenBank flat file into its locus, definition, features and sequence.

Parameter	Type	Required	Notes
text	string	yes	A GenBank flat file (LOCUS … FEATURES … ORIGIN … //).

Convert between FASTA and GenBank (whole sequence, CDS or protein), or export to TSV.

Parameter	Type	Required	Notes
input	string	yes	A FASTA or GenBank record to convert.
from	string	no	Input format; 'auto' sniffs it from the first meaningful line.
to	string	no	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

Statistics for a FASTA or FASTQ file: count, length distribution, N50, GC content and (FASTQ) mean quality.

Parameter	Type	Required	Notes
input	string	yes	FASTA or FASTQ text (raw sequence is treated as single-record FASTA).
qualityOffset	integer	no	FASTQ Phred ASCII offset (33 = Sanger/Illumina 1.8+, 64 = Illumina 1.3–1.7).

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).

Parameter	Type	Required	Notes
fileBase64	string	yes	The binary ABIF (.ab1 / .abi) trace file, base64-encoded.
fileName	string	no	Optional original file name (echoed back).
includeTraces	boolean	no	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 chr

Align a Sanger ABIF read to a reference and report identity plus every mismatch, insertion and deletion.

Parameter	Type	Required	Notes
fileBase64	string	no	The binary ABIF (.ab1 / .abi) trace file, base64-encoded.
read	string	no	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.
reference	string	yes	Expected reference sequence (FASTA or raw).
fileName	string	no	Optional original file name (echoed back).
minCoverage	number	no	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 t

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.

Parameter	Type	Required	Notes
sequence	string	yes	Nucleotide sequence (raw or FASTA; IUPAC accepted).
minOrfAa	integer	no	Minimum ORF length in amino acids (nucleotide input only).
maxOrfs	integer	no	Maximum number of ORFs to return, longest first.
endPrimerLength	integer	no	Length of the naive end primers taken from each end.

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.

Parameter	Type	Required	Notes
sequence	string	yes	Nucleotide sequence (raw or FASTA; IUPAC accepted).
minOrfAa	integer	no	Minimum ORF length in amino acids.
maxOrfs	integer	no	Maximum number of ORFs to return, longest first.
endPrimerLength	integer	no	Length of the naive end primers taken from each end.

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.

Parameter	Type	Required	Notes
entries	object	no	Initial named entries, e.g. {"vector": "...", "insert": "..."}. Optional — you can also add entries later with session_set.

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.

Parameter	Type	Required	Notes
sessionId	string	yes	—
names	array	no	Only return these entries; omit to return all of them.

Add or overwrite named entries in an existing session.

Parameter	Type	Required	Notes
sessionId	string	yes	—
entries	object	yes	Named entries to add/overwrite, e.g. {"insert": "..."}.

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.

Parameter	Type	Required	Notes
sessionId	string	yes	—
tool	string	yes	Name of any non-meta SeqBench tool (not batch, workflow, or another session_* tool).
fromSession	object	no	Map of { toolArgName: sessionEntryName } — resolves each named tool argument from the session before running.
args	object	no	Additional literal arguments, merged with the ones resolved from the session.
writeBack	object	no	Map of { resultFieldName: sessionEntryName } — stores selected fields of the result back into the session under these names.

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)

Parameter	Type	Required	Notes
accession	string	yes	GenBank/RefSeq accession (e.g. NM_000546), UniProtKB accession (e.g. P04637), or Ensembl stable ID (e.g. ENSG00000141510, ENST00000335137).
db	string	no	Database to query; auto-detects from the accession format.
format	string	no	Output format (GenBank is only available for NCBI accessions — UniProt and Ensembl are FASTA-only).

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.

Parameter	Type	Required	Notes
gene	string	no	Gene symbol/name, e.g. "BRCA1". Combined with organism (if given) into a search term.
organism	string	no	Organism name, e.g. "Homo sapiens". Optional; narrows the gene search.
term	string	no	Raw NCBI search term (advanced) — overrides gene/organism when given, e.g. "BRCA1[gene] AND Homo sapiens[orgn]".
db	string	no	—
maxResults	integer	no	Up to 20.

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.

Parameter	Type	Required	Notes
sequence	string	yes	Protein sequence, one-letter code (FASTA header, if any, is stripped).
appl	string	no	Restrict to one member database (e.g. "PfamA"); omit to run EBI's defaults across all of them.
goterms	boolean	no	Include GO-term cross-references.

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.

Parameter	Type	Required	Notes
jobId	string	yes	—

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 ag

Parameter	Type	Required	Notes
sequence	string	yes	Nucleotide sequence (raw or FASTA; IUPAC accepted).
circular	boolean	no	Treat the query as a circular molecule (most plasmids are).
topN	integer	no	How many top-ranked backbone candidates to report.

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

Parameter	Type	Required	Notes
sequence	string	yes	Nucleotide sequence (raw or FASTA; IUPAC accepted).
circular	boolean	no	Treat the query as a circular molecule (most plasmids are).
topN	integer	no	How many top-ranked backbone candidates to report.

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 exac

Parameter	Type	Required	Notes
sequence	string	yes	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
circular	boolean	no	Treat the sequence as a circular plasmid (vs. linear).

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-template

Parameter	Type	Required	Notes
claimedConstruct	string	yes	The final sequence claimed to have been built.
insertTemplate	string	yes	PCR template the insert was amplified from.
insertForwardPrimer	string	yes	Forward primer used to amplify the insert, 5'→3'.
insertReversePrimer	string	yes	Reverse primer used to amplify the insert, 5'→3'.
templateCircular	boolean	no	Treat insertTemplate as circular (e.g. amplifying from a plasmid).
maxPrimerMismatches	integer	no	Mismatches tolerated per primer during PCR prediction (0–10).
expectedFrameStart	integer	no	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.

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 determinist

Parameter	Type	Required	Notes
method	string	yes	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
claimedConstruct	string	yes	The sequence you claim you ended up with.
circular	boolean	no	Treat the product/claimed construct as circular (most plasmids are).
coding	boolean	no	Report amino-acid effects of any mismatch, assuming claimedConstruct is (or contains) a coding sequence.
frameStart	integer	no	1-based reading-frame start on claimedConstruct, used when coding is true.
vector	string	no	Vector sequence (restriction and lic methods; for lic, the LINEARISED vector). Omit if vectorPcr is given.
vectorPcr	object	no	Derive the vector by PCR instead: {template, forwardPrimer, reversePrimer, maxMismatches? (0-10), circular?}.
insert	string	no	Insert sequence (restriction and lic methods). Omit if insertPcr is given.
insertPcr	object	no	Derive the insert by PCR instead: {template, forwardPrimer, reversePrimer, maxMismatches? (0-10), circular?}.
enzyme5	string	no	Insert 5′ enzyme (restriction method).
enzyme3	string	no	Insert 3′ enzyme (restriction method).
vectorEnzyme5	string	no	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.
vectorEnzyme3	string	no	Vector 3′ enzyme (restriction method); defaults to enzyme3.
dephosphorylateVector	boolean	no	The linearised vector was CIP/rSAP-dephosphorylated (restriction method). Affects the self-ligation background warnings, not the product.
fragments	array	no	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 p
fragmentPcrs	array	no	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 instea
names	array	no	Optional labels for each fragment.
overlapLen	integer	no	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 c
mergePreAddedArms	boolean	no	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 re
armTmTarget	number	no	Target annealing Tm (°C) for primer arms.

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

Parameter	Type	Required	Notes
overhangs	array	yes	The candidate 4-base overhangs for one assembly (e.g. ["GGAG","TACT","AATG"]). At least 2, no duplicates.
dataset	string	no	Which real ligation dataset to score against — generic T4 ligase, or an enzyme-specific one-pot dataset if that matches your actual digestion enzyme.
riskThreshold	number	no	Flag a pair as risky when the cross-reaction is at least this fraction of that pair's own total signal.
compareToNamedSet	string	no	Also score this published reference set (see namedSetsAvailable in the output) alongside your candidate set, for comparison.

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.

Parameter	Type	Required	Notes
tool	string	yes	Name of the registered tool to run and save (e.g. "verify_construct").
args	object	yes	Arguments for that tool, exactly as you would pass to it directly.

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 (quer

Parameter	Type	Required	Notes
reference	string	yes	The claimed/expected reference sequence.
reads	string	yes	Raw reads in FASTA or FASTQ format (auto-detected). Up to 2000 reads / 5,000,000 total bp per call.
minSupportingReads	integer	no	Minimum number of reads agreeing on a variant position for it to count as a consensus (candidate real) variant rather than single-read noise.
circular	boolean	no	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 t
platform	string	no	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 hand
minSvSupport	integer	no	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 purpo
minSvLength	integer	no	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
breakpointTolerance	integer	no	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.

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.

Parameter	Type	Required	Notes
query	string	yes	The search query.
max_results	number	no	Maximum number of results to return (default 5, max 10).

Submit up to 1000 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.

Parameter	Type	Required	Notes
ids	array	yes	The ids to map, up to 1000 (e.g. gene symbols, UniProt accessions, Ensembl gene IDs, Entrez GeneIDs, or RefSeq protein accessions, depending on "from").
from	string	yes	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.
to	string	yes	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_
taxId	string	no	NCBI taxonomy id to disambiguate a gene symbol (only used when from="Gene_Name"). Defaults to human (9606) if omitted.

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.

Parameter	Type	Required	Notes
jobId	string	yes	—

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.

Parameter	Type	Required	Notes
symbols	array	yes	Gene symbols to look up, up to 50 (e.g. ["TP53", "BRCA1"]).
sourceSpecies	string	no	Ensembl species slug the symbols belong to (e.g. "human", "mouse"). Defaults to "human".
targetSpecies	string	yes	Ensembl species slug to find homologs in (e.g. "mouse", "rat", "zebrafish", "fruit_fly").
type	string	no	Homology type to return. Defaults to orthologues.

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.

Parameter	Type	Required	Notes
rows	array	yes	Differential expression rows, one per gene.

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.

Parameter	Type	Required	Notes
genes	array	yes	Row (gene) labels.
samples	array	yes	Column (sample) labels.
values	array	yes	genes x samples numeric matrix — one row per gene, in the same order as genes.
clusterRows	boolean	no	Cluster (reorder) genes.
clusterCols	boolean	no	Cluster (reorder) samples.
distanceMetric	string	no	correlation = 1 - Pearson r (the standard expression-heatmap default); euclidean = straight-line distance.
linkage	string	no	average = UPGMA (standard default), complete = farthest-neighbor, single = nearest-neighbor.
zScoreRows	boolean	no	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 s

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 d

Parameter	Type	Required	Notes
genes	array	yes	Query gene symbols (human, e.g. "TP53"). Case-insensitive. Capped at 5000.
background	array	no	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 wh
collections	array	no	Which term collections to test. Defaults to all four.
minTermSize	integer	no	Skip terms/pathways with fewer than this many background genes.
maxTermSize	integer	no	Skip terms/pathways with more than this many background genes (matches clusterProfiler's default).

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. Refuses cleanly — rather t

Parameter	Type	Required	Notes
variant	string	yes	A full HGVS "c." variant description: "<accession or gene symbol>:c.<edit>", e.g. "NM_000546.6:c.215C>G" or "TP53:c.215C>G". Substitution (">"), deletion ("del"), duplication ("dup"), insertion ("ins"

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.

Parameter	Type	Required	Notes
input	string	yes	FASTQ text: records of an '@id' header, sequence, '+' separator and quality line (four lines each).
qualityOffset	integer	no	FASTQ Phred ASCII offset (33 = Sanger/Illumina 1.8+, 64 = Illumina 1.3-1.7).

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.

Parameter	Type	Required	Notes
input	string	yes	FASTQ text: records of an '@id' header, sequence, '+' separator and quality line (four lines each).
qualityOffset	integer	no	FASTQ Phred ASCII offset (33 = Sanger/Illumina 1.8+, 64 = Illumina 1.3-1.7).
qualityThreshold	integer	no	3' quality-trim threshold (Phred score).
minLength	integer	no	Reads shorter than this after trimming are dropped.

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.

Parameter	Type	Required	Notes
accession	string	yes	UniProt accession, e.g. "P04637".

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.

Parameter	Type	Required	Notes
reactions	array	yes	One entry per PCR reaction, up to 96 (a single 96-well plate).

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_

Parameter	Type	Required	Notes
reactions	array	yes	One entry per PCR reaction, up to 96 (a single 96-well plate).
protocolName	string	no	Optional protocol name (used in the script's metadata).

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-sca

Parameter	Type	Required	Notes
reactions	array	yes	One entry per PCR reaction, up to 96 (a single 96-well plate).

One-box variant lookup against MyVariant.info: accepts an rsID, chrom:pos:ref:alt, 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 th

Parameter	Type	Required	Notes
variant	string	yes	An rsID ("rs1042522"), chrom:pos:ref:alt ("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
assembly	string	no	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 c

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.

Parameter	Type	Required	Notes
gene	string	yes	A human gene symbol ("TP53") or Ensembl gene ID ("ENSG00000141510").

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 independentl

Parameter	Type	Required	Notes
gene	string	yes	A human gene symbol ("TP53") or Ensembl gene ID ("ENSG00000141510").

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.

Parameter	Type	Required	Notes
gene	string	yes	A human gene symbol ("TP53") or Ensembl gene ID ("ENSG00000141510").

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 whe

Parameter	Type	Required	Notes
target	string	yes	Forward-strand target DNA (raw or FASTA), with flanking sequence around the intended edit.
editStart	integer	yes	1-based inclusive start of the region being changed.
editEnd	integer	yes	1-based inclusive end of the region being changed. For a pure insertion, set editEnd = editStart - 1.
insertedSeq	string	no	Replacement bases (forward strand). Empty string means a deletion.
rttHomology	integer	no	Homology length (nt) 3' of the edit that the RTT should include (typically 10-16).
pbsLength	integer	no	Optional preferred PBS length to highlight; a full 8-17 nt sweep is always returned.
frameStart	integer	no	Optional 1-based CDS reading-frame start, used only to annotate whether a PAM-blocking mutation would be silent.

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. Coordin

Parameter	Type	Required	Notes
target	string	yes	Forward-strand target DNA (raw or FASTA), with flanking sequence on both sides of the replacement window.
replaceStart	integer	yes	1-based inclusive start of the region being replaced/deleted.
replaceEnd	integer	yes	1-based inclusive end of the region being replaced/deleted. For a pure insertion, set replaceEnd = replaceStart - 1.
newSequence	string	yes	New sequence (forward strand) to install in place of [replaceStart, replaceEnd]. Needs >= 2 bp.
overlapLength	integer	no	Length (bp) of the shared overlap built into both pegRNAs' 3' flaps where they meet and anneal.
pbsLength	integer	no	Optional preferred PBS length to highlight; a full 8-17 nt sweep is always returned.

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 t

Parameter	Type	Required	Notes
sequence	string	yes	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,
cellType	string	no	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.
topN	integer	no	How many top-ranked pegRNAs to return, out of the hundreds enumerated. Max 50.
use5Folds	boolean	no	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.

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 f

Parameter	Type	Required	Notes
target	string	yes	Nucleotide sequence (raw or FASTA; IUPAC accepted).
editor	string	no	Base editor: be3/be4max (CBE, C→T) or abe7.10/abe8e (ABE, A→G).
frameStart	integer	no	Optional 1-based CDS reading-frame start, to classify each edit's amino-acid consequence.
targetPosition	integer	no	Optional 1-based forward-strand position of the base you intend to edit; only guides whose window covers it are returned.

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-neighbour parameters, helix initiation A = −10.8, CT = 100 µM, 100 mM Na⁺). Returns ranked candidates with sense/guide oligos (with UU 3' overhangs)

Parameter	Type	Required	Notes
target	string	yes	Nucleotide sequence (raw or FASTA; IUPAC accepted).
minReynolds	integer	no	Minimum Reynolds score (0–8) to keep; falls back to best-ranked if none qualify.
shRnaLoop	string	no	Loop sequence used when assembling the shRNA cassette.

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 sear

Parameter	Type	Required	Notes
target	string	yes	Nucleotide sequence (raw or FASTA; IUPAC accepted).
length	integer	no	Total gapmer length (nt).
wing	integer	no	Modified-wing length on each side (nt); the central gap = length − 2×wing.

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 do

Parameter	Type	Required	Notes
target	string	yes	Nucleotide sequence (raw or FASTA; IUPAC accepted).
snpPosition	integer	yes	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.
alleleA	string	yes	First allele (single base) — gets the FAM tail.
alleleB	string	yes	Second allele (single base) — gets the HEX tail.
targetCoreTm	number	no	Target Tm (°C) for the allele-specific primer core (before the universal tail).
minAmplicon	integer	no	Minimum amplicon length for the common reverse primer.
maxAmplicon	integer	no	Maximum amplicon length for the common reverse primer.
addSecondaryMismatch	boolean	no	Engineer the internal ARMS destabilising mismatch near the 3' end.

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 compara

Parameter	Type	Required	Notes
sequence	string	yes	Nucleotide sequence (raw or FASTA; IUPAC accepted).

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 hybridisation, mRNA unfolding, spacing, standby site, start-codon binding) for every start codon found. Rates are on an arbitrary scale

Parameter	Type	Required	Notes
sequence	string	yes	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 3,000 nt.
start	number	no	Optional 1-based position; only consider start codons beginning at or after it.
end	number	no	Optional 1-based position; only consider start codons beginning at or before it.
antiShineDalgarno	string	no	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.

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 supp

Parameter	Type	Required	Notes
cds	string	yes	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 3,000 nt.
currentUtr	string	no	Optional: your existing 5' UTR (everything upstream of the start codon). Scored as a baseline so each candidate gets a fold-change against it.
leader	string	no	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.
targetExpression	number	no	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	string	no	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.
limit	number	no	How many ranked candidates to return. 1-60.

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 s

Parameter	Type	Required	Notes
query	string	no	Substring of the vector name or its GenBank definition (case- and punctuation-insensitive, min 2 characters).
category	string	no	Restrict to one category. An unknown category is an error, not an empty result.
feature	string	no	Substring of an annotated feature's label, type or note (min 2 characters), e.g. "T7 promoter", "kanR", "rep_origin".
minLength	integer	no	Smallest vector length in bp.
maxLength	integer	no	Largest vector length in bp.
limit	integer	no	Maximum hits to return. Capped at 100; asking for more is an error, not a silent truncation.

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 unrecognised id is an error carrying the closest nam

Parameter	Type	Required	Notes
id	string	yes	Library id (e.g. "pbr322"), vector name ("pBR322"), or accession ("J01749" / "J01749.1").
includeSequence	boolean	no	Set false for the annotation only — useful for a large BAC where the bases are not the point.

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 lib

Parameter	Type	Required	Notes
query	string	no	Substring of the part name (min 2 characters), e.g. "T7", "AmpR", "SV40 polyA".
kinds	array	no	Restrict to these part kinds (promoter, terminator, origin, RBS, polyA, selection marker, affinity tag, reporter, linker/MCS, …). An unknown kind is an error.
minLength	integer	no	Smallest part length in bp.
maxLength	integer	no	Largest part length in bp.
includeSequence	boolean	no	Include each part's bases (5'→3' on the part's own strand).
limit	integer	no	Maximum hits to return. Capped at 100; asking for more is an error, not a silent truncation.

Run one SeqBench tool over many records at once. input is multi-FASTA or one sequence per line; tool is any batchable tool name; args are shared arguments. Returns a table of per-record results.

Parameter	Type	Required	Notes
tool	string	yes	Batchable tool name (e.g. gc_content, translate).
input	string	yes	Multi-FASTA or one sequence per line.
args	object	no	Shared arguments applied to every record.

Run a multi-tool pipeline over many records. steps is an ordered list of { tool, args?, from? }; each step's chained sequence feeds the next by default. input is multi-FASTA or one sequence per line.

Parameter	Type	Required	Notes
steps	array	yes	—
input	string	yes	Multi-FASTA or one sequence per line.

Where are you running it?

Tool surface

Release history

Workbench MCP

What it does

Quickstart

Where are you running it?

Tool surface

What counts against your monthly calls

Release history

See also