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io.github.cyanheads/ensembl-mcp-server

io.github.cyanheads/ensembl-mcp-server · v0.6.0

Look up genes, sequences, variants, homologs, and cross-database xrefs from Ensembl REST.

MCPremotelocal · npmno credentialsDatabases

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Last check

Reachable, 7 tools, protocol 2025-06-18 · checked 2026-10-17

Test & rating

B 80/100

What it does: 7 tools · 7 read, 0 write · Research & education, Health

Test call ensembl_list_species: failed — timeout (10,812 ms)

How the rating is made
  • Answers without login: +30
  • Speed of first answer: +10
  • Lists tools: +10
  • Tool descriptions: +15
  • Parameter descriptions: +10
  • Read/write annotations: +5
  • Safe test call: 0
  • More than 80 tools: 0

Tested 2026-10-17. Fixed rules, no AI model. Grade A needs a successful real call.

Install

Remote URL
https://ensembl.caseyjhand.com/mcp
Package
registry:   npm
identifier: @cyanheads/ensembl-mcp-server
version:    0.6.0
transport:  stdio

Tools

7 tools listed at last check
  • ensembl_list_species List species supported by Ensembl with display name, common name, assembly, taxon ID, and division. Required discovery step — species names like homo_sapiens are opaque to non-biologists and are the input format every other Ensembl tool expects. Use nameContains to find a species by partial name mat
  • ensembl_lookup_gene Resolve a gene by symbol + species (or by stable ID) to its Ensembl ID, genomic location (chr:start-end:strand), biotype, description, and transcript list. Entry point for most workflows — the stable ID and coordinates returned here are inputs to other tools. Accepts both symbol lookup (BRCA2 + homo
  • ensembl_get_sequence Fetch the DNA, cDNA, CDS, or protein sequence for a gene, transcript, protein, or genomic region. Returns a window of the sequence — the first 10,000 characters by default — with its stable ID, molecule type, and full length. When more follows the window, truncated is true and nextOffset is the offs
  • ensembl_query_region Find genomic features overlapping a chromosomal region: genes, transcripts, variants, regulatory elements, or exons. Returns each feature with its stable ID, type, location, biotype, and name, plus the genome assembly the coordinates are on. Useful for "what's in this locus?" and for seeding follow-
  • ensembl_predict_variant Predict the functional consequences of a sequence variant using the Ensembl Variant Effect Predictor (VEP). Accepts three input formats: HGVS notation (transcript-relative, e.g. ENST00000380152.8:c.2T>A, or genomic, e.g. 13:g.32316462T>A); region+allele (chr:start:end:strand/allele, e.g. 1:65568:655
  • ensembl_get_homology Find orthologs and/or paralogs of a gene across species. Returns each homolog's stable ID, species, homology type (ortholog_one2one, ortholog_one2many, paralog_many2many, etc.), perc_id (percent identity), perc_pos (percent positives), and taxonomy level. Essential for cross-species research — for e
  • ensembl_get_xrefs Retrieve cross-database references for a gene or feature — HGNC, UniProt, EntrezGene, OMIM, RefSeq, Reactome, and others. Returns each xref with its database name, primary ID, display ID, and description. The dbname filter narrows to specific databases; omit to return all xrefs. IDs returned here ch

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