How do I use Ensembl MCP Server?

1. Click on "Install Server". 2. Wait a few minutes for the server to deploy. Once ready, it will show a "Started" state. 3. In the chat, type @ followed by the MCP server name and your instructions, e.g., "@Ensembl MCP Server find the human gene BRCA1 and show me its sequence" That's it! The server will respond to your query, and you can continue using it as needed. Here is a step-by-step guide with screenshots.

Ensembl MCP Server

Model Context Protocol (MCP) server providing access to the Ensembl genomics REST API.

Features

30+ tools for genomic data access:

Gene lookup by symbol or ID
Sequence retrieval
Genetic variants
Cross-species homology
Phenotype data
Regulatory features
Ontology and taxonomy data

Full endpoint documentation available in ENDPOINTS.md.

Installation

From GitHub

npm install git+https://github.com/munch-group/ensembl-mcp.git cd node_modules/ensembl-mcp npm run build

From source

git clone https://github.com/munch-group/ensembl-mcp.git cd ensembl-mcp npm install npm run build

Usage with Claude Desktop

# Using built version claude mcp add ensembl node /path/to/ensembl-mcp/build/index.js # Or from npm global install claude mcp add ensembl npx -y ensembl-mcp

Configuration

Add to your Claude Desktop config:

{ "mcpServers": { "ensembl": { "command": "node", "args": ["/path/to/ensembl-mcp/build/index.js"] } } }

Building

npm run build

Dependencies

@mcp/rest-utils - Shared REST utilities
@modelcontextprotocol/sdk - MCP SDK
zod - Schema validation

License

ISC

This server cannot be installed

-

security - not tested

A

license - permissive license

-

quality - not tested

How are these scores calculated?

Resources

GitHub Repository

Need Help?

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Features

Installation

From GitHub

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Usage with Claude Desktop

Configuration

Building

Dependencies

License

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