# Seqbench Workbench MCP server

Source: https://glimind.com/server/mcp-registry%2Fcom.seqbench%2Fworkbench
Registry id: `mcp-registry/com.seqbench/workbench`
Status: unknown (checked 2026-10-25T04:09:43.394Z)

## Measurements (30 days)

- Uptime: 0%
- Checks: 4
- Outages (90 days): 2

## Install

```json
{
  "mcpServers": {
    "seqbench-workbench-mcp-server": {
      "type": "http",
      "url": "https://seqbench.com/api/mcp"
    }
  }
}
```

Claude Code:

```sh
claude mcp add --transport http seqbench-workbench-mcp-server https://seqbench.com/api/mcp
```

## Tools (114)

- `alphafold_lookup`: 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}
- `aso_design`: Design antisense-oligonucleotide (ASO) gapmers against an mRNA target: scans candidate sites, builds the antisense oligo in the standard 5-10-5 architecture (ch
- `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 bac
- `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 pri
- `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 wi
- `base_editing_design`: 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 a
- `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
- `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 B
- `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 methyl
- `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 se
- `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-Fusio
- `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.
- `codon_optimize`: Codon-optimize a protein (or coding DNA) for an expression host by picking the most-frequent codon per residue.
- `construct_autofix`: Iteratively substitutes synonymous codons to resolve unwanted restriction sites (domestication for Golden Gate), homopolymers, tandem repeats, predicted seconda
- `construct_qc`: Lint a coding DNA sequence for premature stops, internal RBS/polyA motifs, unwanted restriction sites, GC extremes and repeats.
- `crispr_grna_design`: Find and score candidate guide RNAs (protospacer + PAM) in a target DNA for common nucleases (SpCas9, SpCas9-NG, SaCas9, Cas12a). PREDICTED, NOT MEASURED. No he
- `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 (guideSt
- `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
- `crispr_ontarget`: 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 c
- `cross_dimer`: Screen two oligos for the most stable heterodimer (cross-dimer) between them.
- `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 woul
- `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 se
- `double_digest`: Recommend a single NEB buffer (and flag caveats) for digesting with two enzymes in one tube.
- `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,
- `export_echo_picklist`: Generate a downloadable Beckman/Labcyte Echo acoustic-liquid-handler picklist CSV (columns: Source Plate Name, Source Plate Type, Source Well, Destination Plate
- `export_opentrons_protocol`: 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`: 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
- `expression_heatmap_cluster`: Hierarchically cluster a genes x samples expression matrix (UPGMA/average, complete, or single linkage; Euclidean or correlation distance) and return the row/co
- `fastq_qc_report`: FastQC-style deep quality-control report for a FASTQ file: per-base quality and content, GC and length distributions, sequence duplication levels, overrepresent
- `fastq_trim`: 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 (
- `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.
- `functional_enrichment`: Over-representation analysis: test which GO terms (biological process / molecular function / cellular component) and Reactome pathways are statistically enriche
- `gc_content`: GC content, AT content and per-base composition of a sequence.
- `gene_dossier`: A gene/drug-target dossier fanned out to five independent sources in one call: Open Targets (function, tractability, top associated diseases), an NCBI/UniProt p
- `gene_expression`: A gene's tissue-expression fingerprint: per-tissue median TPM from GTEx (v8) and subcellular localization / RNA tissue-specificity / protein class from the Huma
- `gene_model`: 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 ren
- `golden_gate_design`: 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 agai
- `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
- `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 fragm
- `hgvs_convert`: 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 
- `id_map_poll`: 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 (norma
- `id_map_submit`: 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/
- `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' tai
- `kasp_primer_design`: 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
- `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 o
- `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 s
- `motif_finder`: Find (overlapping) occurrences of an IUPAC motif on either strand, allowing mismatches.
- `multiple_sequence_alignment`: Center-star multiple sequence alignment of a multi-FASTA input, with consensus and per-column conservation.
- `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 othe
- `oligo_analysis`: Full oligo analysis: nearest-neighbor Tm/ΔG/ΔH/ΔS plus hairpin and self-dimer screening with base-pair diagrams and warnings.
- `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 
- `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 s
- `ortholog_map`: 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 homo
- `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 — inst
- `pairwise_alignment`: Global (Needleman-Wunsch), local (Smith-Waterman) or semi-global/fitting pairwise alignment of two sequences, with match/mismatch scoring and affine gap costs (
- `parse_genbank`: Parse a GenBank flat file into its locus, definition, features and sequence.
- `parse_sanger_trace`: 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 nam
- `parse_snapgene`: Read a SnapGene .dna file: sequence, topology, every feature with its span, strand, display color and qualifiers (spliced and origin-spanning features kept as s
- `parts_library_search`: Search a parts list harvested from the annotated features of the vector library — promoters, terminators, RBSs, polyA signals, origins, selection markers, affin
- `plasmid_annotate`: Auto-detect common cloning features (promoters, tags, origins, resistance markers, MCS, primers) on both strands. Signatures under 20 bp must match exactly; lon
- `plasmid_deep_annotate`: Annotate a plasmid against pLannotate's open-source feature library — a much larger signature set (GenoLIB parts + Swiss-Prot + FPbase + Rfam, cross-referenced 
- `plasmid_full_report`: One combined view of 'what is this plasmid': recognized common features (from plasmid_annotate), backbone identity / possible chimera (from plasmid_identify), a
- `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
- `prime_editing_design`: Design SpCas9 prime-editing pegRNAs for a substitution, insertion, deletion, or small replacement: for each usable NGG PAM it builds the spacer, a primer-bindin
- `prime_editing_efficiency`: 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, t
- `prime_editing_twin_design`: 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 replace
- `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.
- `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 MG1
- `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 hom
- `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 domai
- `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
- `protein_hydrophobicity`: Sliding-window hydropathy/hydrophobicity profile (ProtScale-style) over a published amino-acid scale.
- `protein_properties`: Protein properties: molecular weight, isoelectric point, GRAVY, extinction coefficient and composition.
- `random_sequence`: Generate a random DNA, RNA or protein sequence, optionally with a target GC content.
- `rbs_design`: 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
- `rbs_predict`: 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 
- `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 —
- `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 pr
- `restriction_sites`: Find restriction enzyme recognition sites in a DNA sequence.
- `reverse_complement`: Reverse, complement and reverse complement of a DNA or RNA sequence.
- `reverse_translate`: Back-translate a protein to DNA (most-frequent codon per organism, or degenerate IUPAC consensus).
- `rna_fold`: Predict an RNA secondary structure by minimum free energy (MFE) using a Zuker dynamic program with Turner 1999 nearest-neighbor stacking energies (no pseudoknot
- `sanger_assemble`: 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 
- `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 cont
- `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
- `sanger_plate_verify`: 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_I
- `sanger_vs_reference`: Align a Sanger ABIF read to a reference and report identity plus every mismatch, insertion and deletion.
- `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}). Use t
- `seqfile_stats`: Statistics for a FASTA or FASTQ file: count, length distribution, N50, GC content and (FASTQ) mean quality.
- `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). Onl
- `sequence_format_convert`: Convert between FASTA and GenBank (whole sequence, CDS or protein), or export to TSV.
- `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.
- `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, or
- `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 po
- `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_r
- `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
- `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 b
- `session_set`: Add or overwrite named entries in an existing session.
- `sirna_design`: 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 T

Measured by Glimind (https://glimind.com): MCP handshake + tool list only, no tool is ever called. CC BY 4.0.