com.seqbench/workbench
com.seqbench/workbench · v1.0.0 · MCP 2025-11-25
Hosted DNA/RNA/protein tools: primers, oligos, PCR, cloning, CRISPR, alignment, batch & pipelines.
Reachability
reachable
checked 2026-07-14 04:27 UTC
Registry status active
Tools pinned 59
fdcb63c36d72
Tools last changed
unchanged since first capture 2026-07-14
Provenance
Registry namespace com.seqbench
(domain verified by the official registry)
Website
https://seqbench.com/mcp
Remote endpoints
https://seqbench.com/api/mcp (streamable-http)
Observed changes
| When (UTC) | Event | Detail |
|---|---|---|
| 2026-07-14 03:16 | first capture | 59 tools pinned |
Pinned tool definitions (59)
| Tool | Description |
|---|---|
| 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-neighbour (SantaLucia 1998) plus Wallace and salt-adjusted estimates, with the length-appropriate recommendation and molecular weights. |
| oligo_analysis | Full oligo analysis: nearest-neighbour 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). |
| 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. |
| 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 nucleotide substitution or an amino-acid codon swap. |
| 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 — see genomesChecked for the exact list). This checks... |
| 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) or restriction–ligation, returning the product and junction primers. |
| plasmid_annotate | Auto-detect common cloning features (promoters, tags, origins, resistance markers, MCS, primers) on both strands. |
| 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. |
| 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. |
| protease_digestion | In-silico protease/chemical digestion: cleave a protein and report each peptide's position, length and neutral mass. |
| codon_optimize | Codon-optimise a protein (or coding DNA) for an expression host by picking the most-frequent codon per residue. |
| codon_adaptation_index | Codon Adaptation Index (CAI) and per-codon relative adaptiveness of a CDS against an expression host, with rare-codon and GC3 analysis. |
| pairwise_alignment | Global (Needleman-Wunsch) or local (Smith-Waterman) pairwise alignment of two sequences with match/mismatch/gap scoring. |
| multiple_sequence_alignment | Center-star multiple sequence alignment of a multi-FASTA input, with consensus and per-column conservation. |
| variant_comparator | Align a query to a reference and call variants (substitutions, insertions, deletions) in HGVS g. notation, with optional coding effects. |
| crispr_grna_design | Find and score candidate guide RNAs (protospacer + PAM) in a target DNA for common nucleases (SpCas9, SpCas9-NG, SaCas9, Cas12a). |
| crispr_offtarget_check | 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. Use this the same... |
| crispr_hdr_donor | 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... |
| parse_genbank | Parse a GenBank flat file into its locus, definition, features and sequence. |
| sequence_format_convert | Convert between FASTA and GenBank (whole sequence, CDS or protein), or export to TSV. |
| seqfile_stats | Statistics for a FASTA or FASTQ file: count, length distribution, N50, GC content and (FASTQ) mean quality. |
| parse_sanger_trace | Decode a Sanger ABIF (.ab1 / .abi) chromatogram: base calls, per-base quality, the four dye-channel traces and peak locations. |
| sanger_vs_reference | Align a Sanger ABIF read to a reference and report identity plus every mismatch, insertion and deletion. |
| characterize_sequence | 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. |
| sequence_report | 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. |
| session_create | 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. |
| session_get | 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. |
| session_set | Add or overwrite named entries in an existing session. |
| session_run | 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... |
| sequence_fetch | 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... |
| sequence_search | 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. |
| protein_annotate_submit | 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. |
| protein_annotate_poll | 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. |
| plasmid_identify | 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 —... |
| plasmid_full_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... |
| plasmid_deep_annotate | Annotate a plasmid against pLannotate's open-source feature library — a much larger signature set (GenoLIB parts + Swiss-Prot, cross-referenced against ~195k Addgene-deposited plasmids) than plasmid_annotate's built-in curated list.... |
| verify_construct | 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,... |
| verify_assembly | Deterministic self-check: given the same method/parts cloning_simulate would use (restriction-ligation, Gibson, or Golden Gate — optionally deriving a part by in-silico PCR first), re-derive the expected WHOLE product and diff it... |
| golden_gate_fidelity | 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... |
| save_permalink | 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}) — no account, no expiry. Use this to cite or share a specific result (e.g. a... |
| sequencing_readback_verify | 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... |
| batch | 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. |
| workflow | 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. |
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