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Unofficial Ensembl MCP Server

@Augmented-Nature

Repository

Basic information

Category

Other

License

MIT license

Transports

stdio

Author

Augmented-Nature

About Unofficial Ensembl MCP Server

A comprehensive Model Context Protocol (MCP) server that provides access to the Ensembl REST API for genomic data, comparative genomics, and biological annotations.

#ensembl#genomics#bioinformatics

Unofficial Ensembl MCP Server config

Add this server to your MCP-compatible client using the configuration below.

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

Unofficial Ensembl MCP Server tools

Tool list not available yet

This listing does not currently have a tool list to display. This does not mean the server has no tools; check its documentation for supported capabilities.

We auto-extract tools from the README. The maintainer can list them under a ## Tools heading to populate this section.

Overview

What is Unofficial Ensembl MCP Server?

An MCP server that provides access to the Ensembl REST API for genomic data, comparative genomics, and biological annotations. Developed by Augmented Nature, it enables gene lookups, sequence retrieval, variant analysis, regulatory features, and more across multiple species through a standardized interface.

How to use Unofficial Ensembl MCP Server?

Install dependencies with npm install, build with npm run build, then configure in Claude Desktop as an MCP server using the command node with arguments pointing to the built index.js. After setup, use natural language queries like "Look up the BRCA2 gene" to access genomic data.

Key features of Unofficial Ensembl MCP Server

  • Gene lookup by Ensembl ID or symbol
  • DNA, CDS, and protein sequence retrieval
  • Variant retrieval and consequence prediction
  • Ortholog and paralog detection across species
  • Access to regulatory elements and motif features
  • Batch processing for multiple genes or regions

Use cases of Unofficial Ensembl MCP Server

  • Look up a gene and retrieve its genomic sequence
  • Find orthologs of a human gene in mouse
  • Get all genetic variants within a specific genomic region
  • Search for genes related to a biological function (e.g., insulin)
  • Obtain assembly information and karyotype for a species

Frequently asked questions

1

What species are supported?

All species available in Ensembl are supported, including vertebrates, plants, fungi, protists, and metazoa. The default species is `homo_sapiens`.

2

What input formats are accepted?

Genomic regions (e.g., `chr1:1000000-2000000`), Ensembl IDs (e.g., `ENSG00000139618`), gene symbols (e.g., `BRCA2`), and RefSeq IDs (e.g., `NM_000059`) are all valid inputs.

3

What are the rate limits?

The server respects Ensembl's guidelines: maximum 15 requests per second, with appropriate delays between batch operations and connection pooling for efficiency.

4

What output formats are available?

Primary formats include JSON, FASTA, GFF, and VCF. Phylogenetic trees support JSON, Newick, and PhyloXML formats.

5

How can I configure the server?

Set environment variables `ENSEMBL_BASE_URL` to override the default API base URL and `REQUEST_TIMEOUT` to change the timeout (default 30000ms). The default species is configurable.

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