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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.

Installation

Add the following to your MCP client configuration file.

Configuration

View docs

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

You can access Ensembl REST API data for genes, transcripts, sequences, variants, regulatory features, and comparative genomics through a dedicated MCP server. This enables you to query, fetch, and analyze diverse genomic data from Ensembl via a standardized MCP interface, integrated with your MCP client workflows.

How to use

Connect to the Ensembl MCP Server using your MCP client. You will interact with a set of named tools that expose Ensembl data through convenient MCP endpoints. Typical tasks include looking up genes, retrieving sequences, finding homologs, predicting variant effects, and mapping coordinates between assemblies. Use the client to invoke tools by their names, supply the required identifiers or regions, and receive structured results that you can integrate into your analyses.

How to install

Prerequisites you need on your machine: a modern Node.js environment and npm installed.

1) Build the server locally if you plan to run it as a local MCP server.

2) Start the MCP server as a local stdio server using the runtime command shown in the configuration snippet.

Configuration and running a local server

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

Additional notes

To use the local server with Claude Desktop, you typically build the server, then configure Claude Desktop to point to the local runtime. The provided flow involves building the server and launching it with the node runtime, using the path to the compiled entry point as shown above.

Supported actions and data access

The Ensembl MCP Server exposes a wide range of capabilities, including gene and transcript lookup, sequence retrieval, regulatory feature access, variant data and consequence prediction, comparative genomics, cross-references, and coordinate mapping. You can perform batch queries and fetch data for multiple regions or genes in a single operation.

Available tools

lookup_gene

Get detailed gene information by stable ID or symbol

get_transcripts

Retrieve all transcripts for a gene with structural details

search_genes

Search genes by name, description, or identifier with filtering options

get_sequence

Get DNA sequence for genomic coordinates or gene/transcript ID

get_cds_sequence

Get coding sequence (CDS) for a transcript

translate_sequence

Translate DNA sequence to protein sequence

get_homologs

Find orthologous and paralogous genes across species

get_gene_tree

Get phylogenetic tree for gene family

get_variants

Get genetic variants in a genomic region

get_variant_consequences

Predict consequences of variants on genes and transcripts

get_regulatory_features

Get regulatory elements in genomic region

get_motif_features

Get transcription factor binding motifs in genomic region

get_xrefs

Get external database cross-references for genes

map_coordinates

Convert coordinates between genome assemblies

list_species

Get list of available species and assemblies

get_assembly_info

Get genome assembly information and statistics

get_karyotype

Get chromosome information and karyotype

batch_gene_lookup

Look up multiple genes simultaneously

batch_sequence_fetch

Fetch sequences for multiple regions or features