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Ensembl MCP Server

Query Ensembl for genes, sequences, genomic features, variant effects, homology, species, and cross-database references over MCP.

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Install Ensembl MCP Server

Pick your client, then add it in one click or paste the config.

STDIONode.js
~/Library/Application Support/Claude/claude_desktop_config.json
claude_desktop_config.json
{
  "mcpServers": {
    "ensembl-mcp-server": {
      "command": "npx",
      "args": [
        "-y",
        "@cyanheads/ensembl-mcp-server"
      ]
    }
  }
}

Settings → Developer → Edit Config, merge this into mcpServers, then fully quit and reopen Claude Desktop.

Install not yet sandbox-tested— we haven't run this command through our automated sandbox yet. Not a red flag; we're working through the catalog.

Overview

ensembl-mcp-server connects MCP clients to the Ensembl REST API for gene, sequence, variant, and comparative-genomics queries. Its seven tools cover species discovery, gene resolution, sequence retrieval, region searches, VEP consequence prediction, homology, and external database references. It also provides gene, transcript, and species resources plus a structured gene-dossier prompt. Use it for biology and bioinformatics workflows involving vertebrates and other Ensembl-supported organisms over STDIO or Streamable HTTP.

Use cases

  • Resolve gene symbols and aliases to Ensembl identifiers
  • Retrieve genomic, transcript, CDS, or protein sequences
  • Inspect genes and variants across genomic regions
  • Predict functional effects for HGVS or dbSNP variants
  • Compare orthologs and connect genes to external databases

Key features

  • Ensembl REST access over MCP
  • Seven gene, sequence, variant, and homology tools
  • Species, gene, and transcript resources
  • Variant Effect Predictor integration
  • STDIO and Streamable HTTP transport
  • Batch gene lookup with alias handling

Tools7

What Ensembl MCP Server lets your agent do. Expand a tool for its parameters.

Self-reported~227 tokens of context

Security & health

What it can reach and how reliably it runs — from our own checks, not the maintainer’s claims.

ActiveLast checked 1d ago

Recent health check succeeded.

9/9 checks healthy over the last 53d

Supply-chain signal

No high-severity advisories surfaced by our automated scan.

Critical 0High 0Medium 0Low 0

Scanned 9d ago via OSV.dev · @cyanheads/ensembl-mcp-server (npm)

Adoption & maintenance

Factual signals from GitHub, npm, and our automated checks — not a rating.

GitHub stars3Stargazers on the source repository.
npm downloads1.4kPackage downloads in the last 30 days.
Last commit6d agoMost recent push to the default branch.
Tools exposed7Callable tools this server registers over MCP.
Directory activity4 viewsConfig copies, upvotes, and views on AllMCPs.

How Ensembl MCP Server works

What ensembl-mcp-server does

Ensembl data becomes available to MCP clients through tools for gene identification, sequence retrieval, genomic-region analysis, variant interpretation, comparative genomics, and cross-database linking. The server supports Ensembl species across divisions including vertebrates, plants, fungi, metazoa, and protists, depending on the endpoint and request.

In addition to tools, it exposes resources for stable-ID gene and transcript records and for supported species. The ensembl_gene_dossier prompt outlines a workflow that starts with a gene symbol, resolves its identifier and location, and then gathers sequence, variant, orthology, and cross-reference information.

How it works

Requests are sent through MCP and translated into calls to the Ensembl REST API. Clients can run the server over STDIO or Streamable HTTP. A hosted endpoint is available at https://ensembl.caseyjhand.com/mcp.

Stable Ensembl identifiers are normalized before requests: a trailing version such as .19 is removed from ENS... identifiers, and responses use the current identifier version. HGVS versions supplied to variant prediction remain intact. IDs from other databases are passed through unchanged.

Gene lookups accept a symbol and species, a stable ID, or batch-style symbol and ID inputs. Symbol resolution includes synonyms and former names, while ambiguous matches are returned with candidates for follow-up. Sequence and region operations support species-qualified coordinates, and sequence results can be read in windows when the requested data is long.

Setup and configuration

The package can be launched with npx:

Terminal
npx -y @cyanheads/ensembl-mcp-server

The repository also publishes a Docker image and provides installation links for Claude Desktop, Cursor, and VS Code. Clients can use the public Streamable HTTP endpoint instead of launching a local process. The available connection styles make the server suitable for local MCP configurations as well as hosted access.

Tools and capabilities

  • ensembl_list_species searches or pages through supported species and returns names, assemblies, taxon IDs, and divisions.
  • ensembl_lookup_gene resolves symbols, aliases, stable IDs, and batches, with optional transcript expansion and canonical-transcript information.
  • ensembl_get_sequence retrieves genomic, cDNA, CDS, or protein sequence by identifier or region, with strand and flanking-sequence options.
  • ensembl_query_region finds genes, transcripts, variants, regulatory features, or exons within a coordinate range, with optional biotype filtering.
  • ensembl_predict_variant sends HGVS, coordinate-and-allele, or dbSNP inputs to Ensembl Variant Effect Predictor.
  • ensembl_get_homology finds orthologs and paralogs, including identity percentages and taxonomy levels.
  • ensembl_get_xrefs returns links to resources such as HGNC, UniProt, EntrezGene, OMIM, RefSeq, and Reactome.

Limitations and notes

Sequence requests are limited to 10 million bases per region, and region feature queries to 5 million bases. Long sequence responses are paged through offsets and maximum lengths. Region queries default to genes and cap returned results unless an uncapped request is made.

The default species endpoint is Ensembl Vertebrates, while other divisions can be selected for species listing. Coordinate naming for mitochondrial sequences differs among organisms. Protein and CDS requests also depend on the selected identifier having a compatible coding record. A non-coding transcript cannot supply protein or CDS output.

Batch gene lookup processes only the first 20 distinct trimmed queries and accepts up to 1,000 submitted items; remaining items must be sent separately. Ensembl stable-ID requests use identifiers without version suffixes, except for versioned HGVS variant input.

Read the full README View source on GitHub

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Frequently Asked Questions about Ensembl MCP Server

ensembl-mcp-server is an MCP server that connects AI clients to the Ensembl REST API. Its main tools list species, resolve genes, retrieve DNA and protein sequences, search genomic regions, predict variant consequences with VEP, find orthologs and paralogs, and return cross-database references.

Run `npx -y @cyanheads/ensembl-mcp-server` to launch it locally. Installation links are also available for Claude Desktop, Cursor, and VS Code, and a Docker image is published. Clients can alternatively connect to the hosted MCP endpoint.

Yes, ensembl-mcp-server has a Cursor installation link and can run through the standard package command. It supports STDIO locally, while the public hosted endpoint provides Streamable HTTP access.

It retrieves genomic DNA, cDNA, CDS, and protein sequences. Inputs can be Ensembl gene, transcript, or protein identifiers, or genomic regions; transcript and protein requests must match the selected sequence type.

Yes, `ensembl_predict_variant` uses Ensembl Variant Effect Predictor to analyze HGVS expressions, coordinate-and-allele inputs, and dbSNP rsIDs, returning the most severe consequence and other prediction data.

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