How do I install the ensembl mcp server?

Use a recorded configuration for your client, replace example credential values and paths, and verify the documented runtime. Restart or reconnect the client, then inspect the available tools.

What credentials does it need?

It reads `MCP_TRANSPORT_TYPE`, `MCP_LOG_LEVEL`, `ENSEMBL_BASE_URL`, `MCP_HTTP_ENDPOINT_PATH` from the environment. Store these in your client's env block or a secrets manager — never commit them to a repository — and grant the narrowest scope that still covers your use case.

SSyncDev

Start a project

Ensembl MCP Server

Look up genes, fetch sequences, predict variant consequences, find orthologs and xrefs via Ensembl.

Remote serverstreamable-http

What is the Ensembl MCP Server?

Look up genes, fetch sequences, predict variant consequences, find orthologs and xrefs via Ensembl.

What the server does

Declarative tool, resource, and prompt definitions — single file per primitive, framework handles registration and validation
Unified error handling — handlers throw, framework catches, classifies, and formats
Pluggable auth: none, jwt, oauth
Swappable storage backends: in-memory, filesystem, Supabase, Cloudflare KV/R2/D1
Structured logging with optional OpenTelemetry tracing
STDIO and Streamable HTTP transports

Credentials and setup notes

Bun v1.3.14 or higher (or Node.js v24+). - No API key required — Ensembl REST is fully public.

More MCP options

Compare MCP servers by category, or browse hosted MCP servers if you prefer an endpoint over a local process.

Maintainer setup documentation.

Recorded tools

Check the linked publisher documentation and your connected client's tool list. Names and availability can vary with the server version and account permissions.

Tool	What it does
ensembl_list_species	List species supported by Ensembl with display name, common name, assembly, taxon ID, and division
ensembl_lookup_gene	Resolve a gene by symbol + species or by stable ID to its Ensembl ID, genomic location, biotype, and transcript list
ensembl_get_sequence	Fetch the DNA, cDNA, CDS, or protein sequence for a gene, transcript, protein, or genomic region
ensembl_query_region	Find genomic features (genes, transcripts, variants, regulatory elements, exons) overlapping a chromosomal region
ensembl_predict_variant	Predict functional consequences of a sequence variant using the Ensembl Variant Effect Predictor (VEP)
ensembl_get_homology	Find orthologs and/or paralogs of a gene across species with percent identity and taxonomy level
ensembl_get_xrefs	Retrieve cross-database references for a gene — HGNC, UniProt, EntrezGene, OMIM, RefSeq, Reactome, and others

How to install the Ensembl MCP Server

{
  "mcpServers": {
    "ensembl-mcp-server": {
      "type": "streamable-http",
      "url": "https://ensembl.caseyjhand.com/mcp"
    }
  }
}

Configuration as documented by the project. Restart the client after saving.

Configuration

Bun v1.3.14 or higher (or Node.js v24+). - No API key required — Ensembl REST is fully public.

Variable	Description	Required
MCP_TRANSPORT_TYPE	Configuration value read at startup.	Optional
MCP_LOG_LEVEL	Configuration value read at startup.	Optional
ENSEMBL_BASE_URL	Endpoint or connection string the server talks to.	Yes
MCP_HTTP_ENDPOINT_PATH	Filesystem location the server is allowed to use.	Optional

Example prompts to try

“Use Ensembl to ensembl list species.”
“Use Ensembl to ensembl lookup gene.”
“Use Ensembl to ensembl get sequence.”

Frequently asked questions

Look up genes, fetch sequences, predict variant consequences, find orthologs and xrefs via Ensembl. Confirm the tools offered by your installed version in the connected client. Tool availability and permissions depend on the server and account configuration.