com.seqbench/workbench
com.seqbench/workbenchHosted DNA/RNA/protein tools: primers, oligos, PCR, cloning, CRISPR, alignment, batch & pipelines.
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Tools · 155
Reverse, complement and reverse complement of a DNA or RNA sequence.
GC content, AT content and per-base composition of a sequence.
Translate a nucleotide sequence to protein (single frame or all six frames; standard code).
Find open reading frames (ATG…stop) across all six frames.
Clean, case-fold, DNA↔RNA convert, reverse and line-wrap a sequence.
Find a motif NOBODY TYPED: given a set of sequences (multi-record FASTA), report the short pattern they share, as a consensus, a position-weight matrix and one site per sequence. This is the opposite …
Find (overlapping) occurrences of an IUPAC motif on either strand, allowing mismatches.
Back-translate a protein to DNA (most-frequent codon per organism, or degenerate IUPAC consensus).
Generate a random DNA, RNA or protein sequence, optionally with a target GC content.
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+ Schild…
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 N…
Full oligo analysis: nearest-neighbor Tm/ΔG/ΔH/ΔS plus hairpin and self-dimer screening with base-pair diagrams and warnings.
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 …
De-novo PCR primer design (Primer3-style penalty picker): enumerate and score candidate primer pairs against length/Tm/GC/3'-clamp/structure constraints.
Design a qPCR assay: primer pairs under qPCR's own constraints (70-150 bp product, tightly matched Tm) each with the best hydrolysis (TaqMan-style) probe that fits between them. The probe sits 6-12 °C…
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.
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…
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 ranke…
Screen two oligos for the most stable heterodimer (cross-dimer) between them.
Self-hosted e-PCR-style screen for off-target amplicons predicted by a primer pair against the background chosen with `background`: the bundled lab genomes (the default — E. coli K-12 MG1655, B. subti…
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 200…
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 exclud…
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 distanc…
Check a list of oligos against the plasmid or template they were designed from, before ordering them. For each oligo: where it primes (3'-anchored, so cloning tails are allowed), on which strand, and …
Find restriction enzyme recognition sites in a DNA sequence.
Recommend a single NEB buffer (and flag caveats) for digesting with two enzymes in one tube.
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 junct…
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 …
Lint a coding DNA sequence for premature stops, internal RBS/polyA motifs, unwanted restriction sites, GC extremes and repeats.
Iteratively substitutes synonymous codons to resolve unwanted restriction sites (domestication for Golden Gate), homopolymers, tandem repeats, predicted secondary structure, cryptic RBS/polyA motifs a…
Predict restriction-digest fragment sizes and their gel migration positions against a chosen DNA ladder.
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 (…
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 lea…
Check the ARRANGEMENT around each coding sequence, which is what decides whether a finished clone expresses at all: a promoter for the named host within reach on the same strand, a Shine-Dalgarno at a…
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 c…
Every combination of interchangeable part plasmids, assembled. Give the alternatives at each position — three promoters, four coding sequences, two terminators, one backbone — and it builds all twenty…
Compare the ways one construct can actually be made — order it whole as a sequence-verified clonal gene, buy only the pieces you cannot amplify, PCR everything out of plasmids you already have, edit o…
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 sequen…
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…
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 …
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 ot…
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 …
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 se…
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 promot…
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-…
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 gi…
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 muc…
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-…
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 …
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, wh…
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 sc…
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 ex…
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 predic…
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 argume…
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 separa…
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 mi…
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, t…
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_quan…
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 annea…
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 obse…
Protein properties: molecular weight, isoelectric point, GRAVY, extinction coefficient and composition.
Sliding-window hydropathy/hydrophobicity profile (ProtScale-style) over a published amino-acid scale. On the Kyte-Doolittle scale it also returns `hydrophobicStretches`: spans where the 19-residue ave…
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 …
Codon-optimize a protein (or coding DNA) for an expression host by picking the most-frequent codon per residue.
Codon Adaptation Index (CAI) and per-codon relative adaptiveness of a CDS against an expression host, with rare-codon and GC3 analysis.
Global (Needleman-Wunsch), local (Smith-Waterman) or semi-global/fitting pairwise alignment of two sequences, with match/mismatch scoring and affine gap costs (Gotoh).
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.
Align a query to a reference and call variants (substitutions, insertions, deletions) in HGVS g. notation, with optional coding effects.
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 dupli…
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 paramete…
A neighbour-joining tree from a multiple ALIGNMENT, as Newick. Distances are corrected pairwise identities over the columns where both rows have a residue — Jukes-Cantor for nucleotides, Poisson for p…
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 inse…
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 …
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/mou…
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 — SpCa…
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…
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…
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,…
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 "emb…
Convert between FASTA and GenBank (whole sequence, CDS or protein), or export to TSV.
Keep a subset of a FASTA file: by length, by a LIST of names (the shape "filter by ID" actually takes — two hundred accessions, not one substring), by a drop list, and by removing records that are the…
Statistics for a FASTA or FASTQ file: count, length distribution, N50, GC content and (FASTQ) mean quality.
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).
Align a Sanger ABIF read to a reference and report identity plus every mismatch, insertion and deletion.
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.
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 q…
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.
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.
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 20…
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 carrie…
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…
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 ident…
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 th…
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 — L…
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 whi…
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 …
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 ever…
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.
Add or overwrite named entries in an existing session.
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 th…
Fetch a public DNA/protein record by accession from NCBI Nucleotide, NCBI Protein, UniProt, or Ensembl (e.g. NM_000546, NP_000537, P04637, ENSG00000141510) — the whole record, or with `start`/`end` ju…
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 …
Find a gene in an assembly by symbol or locus tag and return its sequence with however much flanking DNA you ask for — the step before designing a knockout, a C-terminal tag or an HDR donor, where you…
Submit a protein sequence to EBI InterProScan for domain architecture, family and GO-term annotation, AND for membrane topology and signal-peptide prediction — EBI's default run includes Phobius, TMHM…
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, dedup…
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, sep…
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 regi…
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…
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…
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 orientatio…
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 f…
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-re…
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 ligatio…
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 (…
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/deleti…
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 …
Write the differences a whole-plasmid sequencing consensus shows into the map, keeping the map's annotation: every feature is shifted, grown or shrunk with the edit, a feature whose boundary an edit c…
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 availabl…
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). Return…
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 databas…
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`, …
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 …
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,…
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 backgrou…
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 resolv…
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…
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 opt…
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 acce…
Read a PDB or mmCIF structure file — an RCSB PDB entry, or a model from AlphaFold DB, AlphaFold Server or ColabFold — and report what is in it: every polymer chain with its molecule type, name and one…
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 da…
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 O…
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…
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" / "TP…
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 …
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.
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 (k…
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.
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 ~3…
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…
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…
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 (m…
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…
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…
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 (…
Predict an RNA secondary structure by minimum free energy (MFE) with ViennaRNA's full Turner 2004 loop model at 37 °C (no pseudoknots). Returns the dot-bracket structure, the MFE (kcal/mol), the list …
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 pre…
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 …
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 p…
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 …
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 st…
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, recombinee…
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 st…
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 n…
Run one batchable SeqBench tool over many records. Returns a table of per-record results and typed failures.
Run an ordered multi-tool pipeline over many records. One sequence value can be chained between steps.
Prompts · 4
Design primers for a target and check both structural and background-genome specificity before recommending them.
Verify a plate of Sanger reads against an intended reference and get a per-well pick list without eyeballing each trace.
Remove internal Type IIS sites and other synthesis-risk motifs from a part without changing its protein.
Screen a plasmid of unknown origin against a curated set of common backbones and interpret the result honestly.
How to use
Add to your Claude Desktop / Cursor / Cline MCP config:
{
"mcpServers": {
"com.seqbench/workbench": {
"url": "https://seqbench.com/api/mcp",
"transport": "streamable-http"
}
}
}