Ensembl MCP Server: Install & Setup

Install Ensembl in Claude Code

Remote URL

Claude Code

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

mcp.json (Claude Desktop, Cursor, VS Code, Windsurf)

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

npm

Claude Code

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

mcp.json (Claude Desktop, Cursor, VS Code, Windsurf)

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

Frequently asked questions

What does the Ensembl MCP server do?

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

Is the Ensembl MCP server free?

Yes, most likely. Open source and no paid account or API key is mentioned in the listing. Check the provider for current pricing.

Does Ensembl run locally or remotely?

Local + Remote. Can run locally or be used as a hosted remote server.

How do I add Ensembl to Claude Code?

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

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