# workbench MCP server

Hosted DNA/RNA/protein tools: primers, oligos, PCR, cloning, CRISPR, alignment, batch & pipelines.

## Links
- Registry page: https://www.getdrio.com/mcp/com-seqbench-workbench
- Website: https://seqbench.com/mcp

## Install
- Endpoint: https://seqbench.com/api/mcp
- Auth: Not captured

## Setup notes
- Remote endpoint: https://seqbench.com/api/mcp

## Tools
- reverse_complement (Reverse Complement) - Reverse, complement and reverse complement of a DNA or RNA sequence. Endpoint: https://seqbench.com/api/mcp
- gc_content (GC Content) - GC content, AT content and per-base composition of a sequence. Endpoint: https://seqbench.com/api/mcp
- translate (Translate) - Translate a nucleotide sequence to protein (single frame or all six frames; standard code). Endpoint: https://seqbench.com/api/mcp
- find_orfs (ORF Finder) - Find open reading frames (ATG…stop) across all six frames. Endpoint: https://seqbench.com/api/mcp
- format_sequence (Format Sequence) - Clean, case-fold, DNA↔RNA convert, reverse and line-wrap a sequence. Endpoint: https://seqbench.com/api/mcp
- motif_finder (Motif Finder) - Find (overlapping) occurrences of an IUPAC motif on either strand, allowing mismatches. Endpoint: https://seqbench.com/api/mcp
- reverse_translate (Reverse Translate) - Back-translate a protein to DNA (most-frequent codon per organism, or degenerate IUPAC consensus). Endpoint: https://seqbench.com/api/mcp
- random_sequence (Random Sequence) - Generate a random DNA, RNA or protein sequence, optionally with a target GC content. Endpoint: https://seqbench.com/api/mcp
- melting_temperature (Primer Tm calculator) - Primer/oligo melting temperature: nearest-neighbour (SantaLucia 1998) plus Wallace and salt-adjusted estimates, with the length-appropriate recommendation and molecular weights. Endpoint: https://seqbench.com/api/mcp
- oligo_analysis (Oligo analyzer) - Full oligo analysis: nearest-neighbour Tm/ΔG/ΔH/ΔS plus hairpin and self-dimer screening with base-pair diagrams and warnings. Endpoint: https://seqbench.com/api/mcp
- in_silico_pcr (In-silico PCR) - Predict PCR products for a template and a pair of primers (IUPAC-aware, allows mismatches, handles circular templates). Endpoint: https://seqbench.com/api/mcp
- primer_design (Primer designer) - De-novo PCR primer design (Primer3-style penalty picker): enumerate and score candidate primer pairs against length/Tm/GC/3'-clamp/structure constraints. Endpoint: https://seqbench.com/api/mcp
- dna_molarity (DNA molarity calculator) - 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. Endpoint: https://seqbench.com/api/mcp
- site_directed_mutagenesis (Site-directed mutagenesis designer) - Design site-directed mutagenesis primers (QuikChange overlapping or Q5 back-to-back) for a nucleotide substitution or an amino-acid codon swap. Endpoint: https://seqbench.com/api/mcp
- cross_dimer (Cross-Dimer) - Screen two oligos for the most stable heterodimer (cross-dimer) between them. Endpoint: https://seqbench.com/api/mcp
- primer_specificity (Primer specificity screen) - 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 background/host-genome specificity, NOT whether the primers hit your intended target — pair it with in_silico_pcr against your own template for that. Batchable over candidate REVERSE primers against one fixed forward primer (screen many candidates against a shared partner) — not independent primer-pair batching, which this tool doesn't support. Endpoint: https://seqbench.com/api/mcp
- restriction_sites (Restriction sites) - Find restriction enzyme recognition sites in a DNA sequence. Endpoint: https://seqbench.com/api/mcp
- double_digest (Double digest buffer) - Recommend a single NEB buffer (and flag caveats) for digesting with two enzymes in one tube. Endpoint: https://seqbench.com/api/mcp
- cloning_simulate (Cloning simulator) - Assemble fragments by Gibson/overlap, Golden Gate (Type IIS) or restriction–ligation, returning the product and junction primers. Endpoint: https://seqbench.com/api/mcp
- plasmid_annotate (Plasmid annotator) - Auto-detect common cloning features (promoters, tags, origins, resistance markers, MCS, primers) on both strands. Endpoint: https://seqbench.com/api/mcp
- construct_qc (Construct QC linter) - Lint a coding DNA sequence for premature stops, internal RBS/polyA motifs, unwanted restriction sites, GC extremes and repeats. Endpoint: https://seqbench.com/api/mcp
- construct_autofix (Construct auto-fix (domestication)) - 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 native TypeScript alternative to a constraint-solver sidecar. Endpoint: https://seqbench.com/api/mcp
- virtual_gel (Virtual gel) - Predict restriction-digest fragment sizes and their gel migration positions against a chosen DNA ladder. Endpoint: https://seqbench.com/api/mcp
- protein_properties (Protein Properties) - Protein properties: molecular weight, isoelectric point, GRAVY, extinction coefficient and composition. Endpoint: https://seqbench.com/api/mcp
- protein_hydrophobicity (Hydrophobicity Profile) - Sliding-window hydropathy/hydrophobicity profile (ProtScale-style) over a published amino-acid scale. Endpoint: https://seqbench.com/api/mcp
- protease_digestion (Protease Digestion) - In-silico protease/chemical digestion: cleave a protein and report each peptide's position, length and neutral mass. Endpoint: https://seqbench.com/api/mcp
- codon_optimize (Codon optimiser) - Codon-optimise a protein (or coding DNA) for an expression host by picking the most-frequent codon per residue. Endpoint: https://seqbench.com/api/mcp
- codon_adaptation_index (CAI analyser) - Codon Adaptation Index (CAI) and per-codon relative adaptiveness of a CDS against an expression host, with rare-codon and GC3 analysis. Endpoint: https://seqbench.com/api/mcp
- pairwise_alignment (Pairwise Alignment) - Global (Needleman-Wunsch) or local (Smith-Waterman) pairwise alignment of two sequences with match/mismatch/gap scoring. Endpoint: https://seqbench.com/api/mcp
- multiple_sequence_alignment (Multiple Sequence Alignment) - Center-star multiple sequence alignment of a multi-FASTA input, with consensus and per-column conservation. Endpoint: https://seqbench.com/api/mcp
- variant_comparator (Variant Comparator) - Align a query to a reference and call variants (substitutions, insertions, deletions) in HGVS g. notation, with optional coding effects. Endpoint: https://seqbench.com/api/mcp
- crispr_grna_design (CRISPR gRNA designer) - Find and score candidate guide RNAs (protospacer + PAM) in a target DNA for common nucleases (SpCas9, SpCas9-NG, SaCas9, Cas12a). Endpoint: https://seqbench.com/api/mcp
- crispr_offtarget_check (CRISPR guide off-target 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 way primer_specificity is used: a useful sanity check within the covered organisms, not a clearance guarantee for a mammalian expression host. Endpoint: https://seqbench.com/api/mcp
- crispr_hdr_donor (HDR donor designer) - 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 confirm the edit), reusing the same primer-design engine as primer_design. Endpoint: https://seqbench.com/api/mcp
- parse_genbank (GenBank Parser) - Parse a GenBank flat file into its locus, definition, features and sequence. Endpoint: https://seqbench.com/api/mcp
- sequence_format_convert (Sequence Format Converter) - Convert between FASTA and GenBank (whole sequence, CDS or protein), or export to TSV. Endpoint: https://seqbench.com/api/mcp
- seqfile_stats (FASTA/FASTQ Stats) - Statistics for a FASTA or FASTQ file: count, length distribution, N50, GC content and (FASTQ) mean quality. Endpoint: https://seqbench.com/api/mcp
- parse_sanger_trace (Sanger Trace Parser) - Decode a Sanger ABIF (.ab1 / .abi) chromatogram: base calls, per-base quality, the four dye-channel traces and peak locations. Endpoint: https://seqbench.com/api/mcp
- sanger_vs_reference (Sanger vs Reference) - Align a Sanger ABIF read to a reference and report identity plus every mismatch, insertion and deletion. Endpoint: https://seqbench.com/api/mcp
- characterize_sequence (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. Endpoint: https://seqbench.com/api/mcp
- sequence_report (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. Endpoint: https://seqbench.com/api/mcp
- session_create (Create a design session) - 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. Endpoint: https://seqbench.com/api/mcp
- session_get (Read a design session) - 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. Endpoint: https://seqbench.com/api/mcp
- session_set (Write to a design session) - Add or overwrite named entries in an existing session. Endpoint: https://seqbench.com/api/mcp
- session_run (Run a tool using session entries) - 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. Endpoint: https://seqbench.com/api/mcp
- sequence_fetch (Fetch sequence by accession) - 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) — Ensembl's own default for each ID type. Endpoint: https://seqbench.com/api/mcp
- sequence_search (Search sequence databases by name) - 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. Endpoint: https://seqbench.com/api/mcp
- protein_annotate_submit (Submit a protein for domain/GO annotation) - 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. Endpoint: https://seqbench.com/api/mcp
- protein_annotate_poll (Poll a protein annotation job) - 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. Endpoint: https://seqbench.com/api/mcp
- plasmid_identify (Identify an unknown plasmid) - 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 against Addgene's ~100k-plasmid catalog or PlasmidScope's 850k+ — a curated-set screen only. Endpoint: https://seqbench.com/api/mcp
- plasmid_full_report (Plasmid full report (identity + features + unexplained regions)) - 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 real gene-of-interest legitimately has no curated-feature match. Endpoint: https://seqbench.com/api/mcp
- plasmid_deep_annotate (Deep plasmid annotation (pLannotate)) - 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/low-identity hits rather than only exact signature matches. Each feature carries its percent identity, reference coverage and a fragment flag so you can judge a weak hit. Runs a multi-second search on a shared service and is therefore rate limited (see 429/503); use plasmid_annotate for an instant, unmetered first pass. Endpoint: https://seqbench.com/api/mcp
- verify_construct (Verify a claimed 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, at what identity, and with exact mismatch positions if not. Optionally also checks for a premature stop in a declared reading frame. This re-derives from the claim's own stated inputs; it does not review the claim's prose. Endpoint: https://seqbench.com/api/mcp
- verify_assembly (Verify a full assembly recipe) - 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 against a claimed final sequence. Returns pass/fail plus the exact position and nature of any discrepancy — not an opinion, the same deterministic simulation SeqBench already runs, run a second time as a check. See verify_construct for a narrower, insert-only check that doesn't require declaring the vector/enzymes/method. Endpoint: https://seqbench.com/api/mcp
- golden_gate_fidelity (Golden Gate overhang 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 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 percentages for named sets (their exact formula isn't disclosed anywhere accessible). Endpoint: https://seqbench.com/api/mcp
- save_permalink (Save a permanent shareable link) - 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. Endpoint: https://seqbench.com/api/mcp
- sequencing_readback_verify (Sequencing read-back verification) - 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). Complements verify_construct/verify_assembly: those re-derive what a design SHOULD produce from its own stated inputs; this checks what a real sequencer actually read back. Endpoint: https://seqbench.com/api/mcp
- web_search (Search the web) - 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. Endpoint: https://seqbench.com/api/mcp
- id_map_submit (Submit a batch gene/protein ID mapping job) - 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. Endpoint: https://seqbench.com/api/mcp
- id_map_poll (Poll a batch ID mapping job) - 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. Endpoint: https://seqbench.com/api/mcp
- ortholog_map (Find orthologs/paralogs for gene symbols across species) - 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. Endpoint: https://seqbench.com/api/mcp
- volcano_plot_data (Volcano plot data) - 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. Endpoint: https://seqbench.com/api/mcp
- expression_heatmap_cluster (Expression heatmap clustering) - 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. Endpoint: https://seqbench.com/api/mcp
- functional_enrichment (Functional enrichment (GO + Reactome)) - 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 does not permit bundling gene sets). Endpoint: https://seqbench.com/api/mcp
- hgvs_convert (HGVS Variant Converter (c. <-> g. <-> p.)) - 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 than guessing — for circular/mitochondrial genomes, RNA-level or protein-level input, uncertain/mosaic syntax, splice-junction-adjacent or inversion protein effects, and non-MANE/non-Ensembl transcripts. Endpoint: https://seqbench.com/api/mcp
- fastq_qc_report (FASTQ Deep QC Report) - 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. Endpoint: https://seqbench.com/api/mcp
- fastq_trim (FASTQ Adapter & Quality Trimmer) - 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. Endpoint: https://seqbench.com/api/mcp
- alphafold_lookup (Look up an AlphaFold structure prediction) - 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. Endpoint: https://seqbench.com/api/mcp
- export_plate_layout (PCR 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 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. Endpoint: https://seqbench.com/api/mcp
- export_opentrons_protocol (Opentrons protocol export) - 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_20ul, opentrons_24_tuberack_nest_1.5ml_snapcap, nest_12_reservoir_15ml, p20_single_gen2) and the confirmed load_labware/load_instrument/transfer method signatures. Master-mix/primer/template/water volumes are clearly-labeled placeholder constants at the top of the script — this is a starting point to review and adapt for your own enzyme and instrument, not a certified ready-to-run protocol. Endpoint: https://seqbench.com/api/mcp
- export_echo_picklist (Echo picklist export) - 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-scale PCR reaction (master mix 2500 nL, each primer 250 nL, template 250 nL, water 1750 nL) — a commonly used acoustic-dispensing miniaturization scale, not a universal standard; rescale the volumes for your own protocol. Source/Destination Plate Type uses a placeholder Echo plate-type code (384PP_AQ_BP) — replace with the exact type from your own Echo Plate Type Library. Endpoint: https://seqbench.com/api/mcp
- variant_annotate (Variant Annotator) - 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 that source has no data, never silently omitted. See the result's own "caveats" for real data-freshness limits (frozen gnomAD/CADD snapshots, periodic ClinVar snapshot). Endpoint: https://seqbench.com/api/mcp
- gene_model (Gene Model (Exon/CDS Structure)) - 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. Endpoint: https://seqbench.com/api/mcp
- gene_dossier (Gene/Target 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 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 independently — a down source returns null/empty for its own section rather than failing the whole call, and every failure is listed in "sourceErrors" rather than silently omitted. Endpoint: https://seqbench.com/api/mcp
- gene_expression (Gene Expression Fingerprint) - 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. Endpoint: https://seqbench.com/api/mcp
- prime_editing_design (Prime Editing Studio (pegRNA)) - 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 where the edit destroys the pegRNA's own PAM (preventing re-nicking of the edited allele) are ranked first. Off-target activity is not evaluated (no in-browser reference genome). Endpoint: https://seqbench.com/api/mcp
- prime_editing_twin_design (twinPE Studio (dual pegRNA)) - 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. Off-target activity is not evaluated (no in-browser reference genome). Endpoint: https://seqbench.com/api/mcp
- base_editing_design (Base Editing Designer) - 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 first. Handles both strands (a C→T on the protospacer of a reverse-strand guide is reported as the forward-strand G→A). Endpoint: https://seqbench.com/api/mcp
- sirna_design (siRNA / shRNA Designer) - Design siRNA duplexes against an mRNA target using the established Reynolds (2004) 8-criteria score and the Ui-Tei (2004) rules, plus a siDirect-style seed-duplex Tm off-target flag (≥21.5 °C). Returns ranked candidates with sense/guide oligos (with UU 3' overhangs) and, per candidate, a ready shRNA cassette (sense–loop–antisense–Pol III terminator). Heuristic sequence rules only — no RNA-folding accessibility model and no transcriptome-wide off-target search. Endpoint: https://seqbench.com/api/mcp
- aso_design (ASO Gapmer Designer) - 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 search. Endpoint: https://seqbench.com/api/mcp
- kasp_primer_design (KASP / ARMS Allele-Specific Primers) - 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 the natural allele mismatch (strong↔weak), and one common downstream reverse primer sized to a chosen amplicon range. Reuses the site's nearest-neighbor Tm engine. Endpoint: https://seqbench.com/api/mcp
- rna_fold (RNA Secondary Structure (MFE)) - 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 comparative estimate, not a lab-grade absolute. Endpoint: https://seqbench.com/api/mcp
- batch (Batch (one tool over many records)) - 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. Endpoint: https://seqbench.com/api/mcp
- workflow (Batch workflow (multi-tool pipeline)) - 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. Endpoint: https://seqbench.com/api/mcp

## Resources
Not captured

## Prompts
- design_specific_primers - Design specific PCR primers Design primers for a target and check both structural and background-genome specificity before recommending them.
- verify_clone_batch - Verify a plate of Sanger reads Verify a plate of Sanger reads against an intended reference and get a per-well pick list, without eyeballing each trace by hand.
- domesticate_for_golden_gate - Domesticate a part for Golden Gate Remove internal Type IIS sites (and other synthesis-risk motifs) from a part, without changing its protein.
- identify_unknown_plasmid - Identify an unknown plasmid Screen a plasmid of unknown origin against a curated set of common backbones and interpret the result honestly.

## Metadata
- Owner: com.seqbench
- Version: 1.0.0
- Runtime: Streamable Http
- Transports: HTTP
- License: Not captured
- Language: Not captured
- Stars: Not captured
- Updated: Jul 6, 2026
- Source: https://registry.modelcontextprotocol.io