SeqBench MCP server

• Registry namecom.seqbench/workbenchverified in the MCP registry

The registry name sits under seqbench.com. The registry only lets a publisher use that namespace after proving control of the domain through DNS or HTTP.

• Stateanswerschecked 2026-10-16
• Tools151
• Server calls itselfcom.seqbench/workbench
• Server version2.0.0
• Protocol version2025-06-18

On 2026-10-16 the server answered initialize and tools/list without a sign-in. First answer in 43 ms.

• Answeredmeasuring1 of the 7 daily checks it takes to print a share
• Median first answer98 ms
• Space in an agent's context≈ 70,136 tokensthe definitions of all its tools (155), which an agent carries on every turn
• Tool definitionsA · 98 of 100

• Parameters without a description: in 17 of 155

A program checks the server once a day: initialize and tools/list, no model. Tokens are the definitions' length at about four characters a token. The grade averages six checks of every tool's name, description, schema and annotations; it says how well the tools are described, not whether they work. The state of vendors' MCP servers: method and numbers →

• reverse_complement

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

• gc_content

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

• translate

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

• find_orfs

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

• format_sequence

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

• motif_finder

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

• reverse_translate

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

• random_sequence

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

• melting_temperature

  Primer/oligo melting temperature: nearest-neighbor (SantaLucia 1998) at the supplied reaction conditions, recommended from 14 nt up, with the Wallace rule for shorter oligos, a fixed-100 mM-Na+ Schildkraut-Lifson reference estimate, and…

• annealing_temperature

  Annealing temperature and a full cycling program for a primer PAIR, under the rule the polymerase's own vendor publishes — which is not one rule, and is only defined against the vendor's own Tm. For NEB products the Tm is computed exactly…

• oligo_analysis

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

• in_silico_pcr

  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…

• primer_design

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

• qpcr_assay_design

  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 above the warmer primer, never begins…

• dna_molarity

  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.

• site_directed_mutagenesis

  Design site-directed mutagenesis primers (QuikChange overlapping or Q5 back-to-back) for a base substitution, an amino-acid codon swap, or an insertion/deletion/delins. The edit can be given as fields or, more simply, by NAME in…

• oligo_pool_screen

  Screen a whole set of oligos you already have — every pair for cross-dimers, every oligo for its own hairpin and self-dimer, and the set for duplicates and Tm spread — and get back the conflicts ranked rather than a table of every…

• cross_dimer

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

• primer_specificity

  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…

• oligo_cofold

  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…

• barcode_design

  Build a set of DNA barcodes that are pairwise at least a chosen edit distance apart, so a read error cannot turn one barcode in the pool into another. Honours a GC window, a homopolymer cap and excluded motifs (the restriction sites you…

• barcode_audit

  Take a set of barcodes and report the minimum edit distance in it, which pairs sit at that distance, any duplicates, the GC range and the longest homopolymer. The pairs are the point: 'minimum distance 2' is a number, and 'these two…

• oligo_order_check

  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 which bases disagree with the map…

• restriction_sites

  Find restriction enzyme recognition sites in a DNA sequence.

• double_digest

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

• cloning_simulate

  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…

• plasmid_annotate

  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…

• construct_qc

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

• construct_autofix

  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…

• virtual_gel

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

• ligation_setup

  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…

• gel_band_size

  Calibrate a gel lane against a marked DNA ladder and read the size of any other band from how far it ran. Migration distance is approximately linear in log(size) over a gel's resolving range, so a least-squares line through the marked…

• golden_gate_from_parts

  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…

• build_route_plan

  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 one plasmid by mutagenesis, or anneal…

• assembly_outcomes

  Enumerate the specific wrong plasmids a multi-part Golden Gate or Gibson assembly can produce — a part dropped, inverted, duplicated, two parts swapped, the backbone self-circularized — as full sequences, ranked by how few independent…

• diagnostic_digest

  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…

• repeat_instability

  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…

• nonrepetitive_parts_find

  Given a toolbox of genetic parts, return the largest subset in which no two parts share more than a chosen length of sequence — on either strand. Parts that share a long stretch recombine into each other in a multi-part assembly and are…

• nonrepetitive_parts_design

  Build a set of new genetic parts that match a degenerate (IUPAC) template and share more than a chosen length with nothing — not each other, not themselves, not a background sequence you supply. This is how a toolbox of promoters, RBSs…

• operon_scan

  Scan a multi-gene construct, on both strands, for the sequence that quietly breaks operons: promoter-like -35/-10 pairs (including ones pointing backwards, which make antisense RNA), Shine-Dalgarno sequences positioned in front of an…

• operon_design

  Build a polycistronic operon from a promoter, a list of CDSs with their RBSs, spacers and a terminator — optionally recoding every CDS for a host — then scan the ASSEMBLED molecule for internal promoters, Shine-Dalgarno sequences…

• synthesis_complexity

  Measure the sequence features gene-synthesis vendors screen on — repeats (the single largest cause of synthesis failure), GC extremes, GC swings between adjacent windows, homopolymer runs and hairpin-forming inverted repeats — and report…

• band_traceback

  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…

• sanger_indel_spectrum

  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…

• outcome_deconvolve

  Decompose one Sanger trace into fractions over a set of candidate molecules — the intended construct, the empty backbone, a double insert, a flipped part — instead of onto a generic indel ladder. Non-negative least squares against the…

• trace_secondary_peaks

  Read a chromatogram for what the basecaller did not report: positions where a second dye is present under the called base (a heterozygote, or a contaminating template), and bases still visible in the scan past where base calling stopped…

• trace_diagnose

  Diagnose a failing Sanger chromatogram: the longest usable window (Mott trimming), whether there is signal above the noise at all, whether more than one molecule is in the tube and from which base, whether quality collapsed at a…

• primer_site_accessibility

  Fold the template around each place a primer binds, at the annealing temperature and under DNA parameters, and report how much of the primer's own footprint sits inside a helix. Primer design tools score the oligo — its Tm, its hairpin…

• promoter_predict

  Scan DNA for E. coli sigma-70 promoters and estimate each one's transcription initiation rate, with the free-energy terms it is built from: the -35 and -10 boxes, the spacer, the discriminator, the extended -10 and the initial transcribed…

• promoter_library_design

  Build a set of sigma-70 promoters that (a) share no more than a chosen length of sequence with each other, so the library does not recombine with itself once integrated, and (b) span a range of predicted transcription rates, picked as an…

• cloning_next_observation

  Rank every observation you have not yet made by how many open causes it settles WHICHEVER WAY IT COMES OUT, then return the smallest set of observations that settles all of them. Takes the same arguments as cloning_diagnose. The ranking…

• read_placement_plan

  Given the molecules a cloning reaction could have produced and the sequencing primers you could use, work out which primers separate which pairs of candidates — and return the smallest set that separates every pair any of them can. Scores…

• base_edit_quant

  Quantify CBE/ABE base editing from a pair of Sanger traces — an unedited control and the edited pool — without NGS. At each editable position in the activity window the edited trace is treated as a mixture of the unedited and converted…

• sanger_knockin_quant

  Measure the rate of a SPECIFIC intended edit from a pair of Sanger traces — an unedited control and the edited pool — by decomposing the edited trace onto three things at once: the wild-type allele, the intended edited allele, and the…

• editing_plate_quantify

  Quantify a whole plate of edited samples against ONE untreated control trace and return a single sortable table — the plate-scale form of sanger_indel_spectrum, base_edit_quant and sanger_knockin_quant, chosen with `mode`. Each sample…

• multiplex_panel_design

  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…

• cloning_diagnose

  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…

• protein_properties

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

• protein_hydrophobicity

  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 average stays at or above 1.6, the line…

• protease_digestion

  In-silico protease/chemical digestion: cleave a protein and report each peptide's position, length and neutral mass. CNBr masses assume terminal Met becomes homoserine lactone; the sequence retains M and the response labels the…

The first 60 of 151, as the server listed them.