io.github.cyanheads/ensembl-mcp-server

up checked 2026-11-11T02:37:48.608Z

Unclaimed · Unverified

Agent searches it appeared in, last 30 days: 0. Run this server? Claim the listing: verified label, uptime alerts and analytics.

Publisher-provided description

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

Summary by lookupd

Queries Ensembl for gene lookup, sequences, homologs, variant effect prediction, genomic regions, and cross-database references across…

Install

Claude Code, remote (streamable-http)

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

Claude Code, npm package (stdio)

claude mcp add ensembl-mcp-server -- npx -y @cyanheads/ensembl-mcp-server

Claude Code, npm package (stdio)

claude mcp add ensembl-mcp-server -- npx -y @cyanheads/ensembl-mcp-server

Codex, remote (streamable-http)

codex mcp add ensembl-mcp-server --url https://ensembl.caseyjhand.com/mcp

Codex, npm package (stdio)

codex mcp add ensembl-mcp-server -- npx -y @cyanheads/ensembl-mcp-server

Codex, npm package (stdio)

codex mcp add ensembl-mcp-server -- npx -y @cyanheads/ensembl-mcp-server

Cursor, remote (streamable-http) → .cursor/mcp.json

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

Cursor, npm package (stdio) → .cursor/mcp.json

{
  "mcpServers": {
    "ensembl-mcp-server": {
      "command": "npx",
      "args": [
        "-y",
        "@cyanheads/ensembl-mcp-server"
      ]
    }
  }
}

Cursor, npm package (stdio) → .cursor/mcp.json

{
  "mcpServers": {
    "ensembl-mcp-server": {
      "command": "npx",
      "args": [
        "-y",
        "@cyanheads/ensembl-mcp-server"
      ]
    }
  }
}

Other clients: docs. Or tell your agent: Set up lookupd for me: read https://lookupd.com/agent.md and follow it.

Tools (7 tools)

Publisher-provided text

• 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 ar
• 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. Entr
• 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
• ensembl_query_region Find genomic features overlapping a chromosomal region: genes, transcripts, variants, regulatory elements, or exons. Returns each feature with its stable ID, ty
• ensembl_predict_variant Predict the functional consequences of a sequence variant using the Ensembl Variant Effect Predictor (VEP). Accepts three input formats: HGVS notation (transcri
• 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_
• 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 na

Details

• Version: 0.7.1
• Transports: streamable-http, stdio
• Uptime (7 days): 100%
• Median latency: 660 ms
• First indexed: 2026-11-01T09:25:58.567Z
• Last seen in registry: 2026-11-01T09:25:58.746Z
• Repository: https://github.com/cyanheads/ensembl-mcp-server

Badge for your README

Shows this live status and links here; updates hourly.

[![lookupd status](https://lookupd.com/badge/io.github.cyanheads/ensembl-mcp-server.svg)](https://lookupd.com/servers/io.github.cyanheads/ensembl-mcp-server)

• 62092 servers
• Last crawl: 2026-11-11T17:38:11.606Z
• API base: https://api.lookupd.com
• MCP URL: https://api.lookupd.com/mcp