Ensembl MCP Server

An MCP server that exposes the Ensembl REST API so Claude can look up genes and transcripts, fetch sequences, interpret variants, and run comparative-genomics queries from natural language.

   
Type MCP server
Supplier effieklimi
Availability GA
Pricing Free / OSS (MIT). Ensembl REST API needs no key; the Smithery installer path requires a free Smithery key.
Capabilities Read-only — queries the public Ensembl REST API

How to install

  • Also packaged in the SciAgent-Skills collection (jaechang-hits (community OSS, CC BY 4.0)): clone jaechang-hits/SciAgent-Skills and run /plugin install sciagent-skills in Claude Code (or copy skills/genomics-bioinformatics/databases/ensembl-database into ~/.claude/skills/). The server is published to npm as ensembl-mcp-server and runs over stdio via npx.

  • Claude Code — direct MCP add (stdio; Claude Code launches the process itself, so don’t run npx separately): 
    claude mcp add --transport stdio ensembl -- npx -y ensembl-mcp-server
  • Claude Desktop — add to claude_desktop_config.json: 
    {
  "mcpServers": {
    "ensembl": { "command": "npx", "args": ["-y", "ensembl-mcp-server"] }
  }
}
  • Either client — via Smithery (requires a free Smithery key; replace your-smithery-key with the key from your Smithery dashboard): 
    npx -y @smithery/cli@latest install @effieklimi/ensembl-mcp-server --client claude --key your-smithery-key

Requires Node.js. No Ensembl account or API key is needed for the REST API itself.

What it does

Ten tools spanning the Ensembl REST API:

  • ensembl_lookup — ID/symbol translation, cross-references, variant recoding
  • ensembl_sequence — DNA, RNA, and protein sequence retrieval
  • ensembl_feature_overlap — genes/transcripts/regulatory elements overlapping a region
  • ensembl_mapping — coordinate conversion and assembly lift-over
  • ensembl_variation — variant lookup, VEP consequences, phenotype mapping
  • ensembl_compara — comparative genomics, homology, gene trees
  • ensembl_regulatory — regulatory features, binding matrices, annotations
  • ensembl_protein_features — protein domains and functional sites
  • ensembl_ontotax — ontology and taxonomy traversal
  • ensembl_meta — server metadata, species lists, release info

Primary use cases: Gene/transcript annotation lookup, sequence retrieval, variant consequence prediction, cross-species homology, genome-coordinate lift-over.

Notes

Read-only wrapper over the public Ensembl REST API; no write operations. A separate hosted HTTP variant exists via the Pipeworx gateway (claude mcp add --transport http ensembl https://gateway.pipeworx.io/ensembl/mcp), and Augmented-Nature/Ensembl-MCP-Server is an alternative implementation — the npm ensembl-mcp-server package documented above is the most direct install for Claude.

Sources

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