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io.github.cyanheads/ensembl-mcp-server

io.github.cyanheads/ensembl-mcp-server · v0.6.1

Measured by MCP Station

Description written by the publisher, not verified

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

Connect

claude mcp add --transport http ensembl-mcp-server https://ensembl.caseyjhand.com/mcp

{
  "mcpServers": {
    "ensembl-mcp-server": {
      "url": "https://ensembl.caseyjhand.com/mcp"
    }
  }
}

Tools as reported by the server

• 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.), percId (percent identity), percPos (percent positives), and taxonomy level. Essential for cross-species research — for exa
• 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. By default only the requested object level is queried; all_levels=true includes transcript and

Tool changes

• 2026-10-20: ensembl_list_species, ensembl_lookup_gene, ensembl_get_sequence, ensembl_query_region, ensembl_predict_variant, ensembl_get_homology, ensembl_get_xrefs
• 2026-10-16: ensembl_list_species, ensembl_lookup_gene, ensembl_get_sequence, ensembl_query_region, ensembl_predict_variant, ensembl_get_homology, ensembl_get_xrefs

Repository · JSON · Text for agents · Registry updated 2026-10-19