Ensembl MCP Server - install, status & alternatives [2026]

01 · Install Ensembl MCP Server

before you install - you'll need

Set MCP_TRANSPORT_TYPE, MCP_LOG_LEVEL before connecting.

Claude Code

claude mcp add cyanheads-ensembl-mcp-server --transport http https://ensembl.caseyjhand.com/mcp

Claude Desktop / Cursor / VS Code - add to config

{
  "mcpServers": {
    "cyanheads-ensembl-mcp-server": {
      "url": "https://ensembl.caseyjhand.com/mcp"
    }
  }
}

Same JSON for Cursor. For VS Code, rename the top-level key from `mcpServers` to `servers`.

Using another client? Same JSON, different key

Claude Desktop · mcpServers

Cursor · mcpServers

VS Code · servers

Windsurf · mcpServers

Zed · context_servers

Cline · mcpServers

Roo Code · mcpServers

Continue · mcpServers

LibreChat · mcpServers

Gemini CLI · mcpServers

Codex CLI · mcp_servers

Full setup guides: every client.

02 · Evidence

https://ensembl.caseyjhand.com/mcp

transport: streamable-http

endpoint alive - responded to MCP initialize · probed 2026-09-30

Security posture

What to check before giving this server access to your agent - from the registry, GitHub, and our own probes. We don't score safety; we show what's verifiable.

runs as local process (stdio) - runs on your machine with your user's permissions · remote - your agent's requests go to ensembl.caseyjhand.com

endpoint auth accepted our unauthenticated MCP initialize - no credentials needed to connect

license Apache-2.0 - declared in the repository

npm package @cyanheads/ensembl-mcp-server - published under the repo owner's npm scope (@cyanheads)

registry namespace io.github.cyanheads is GitHub-verified and matches the repo owner

03 · What Ensembl MCP Server can do

Prose above is summarized from the project's README and registry record - no invented capabilities.

What you can build

With this server connected, an agent can list species supported by Ensembl with display name, common name, assembly, taxon ID, and division, resolve a gene by symbol + species or by stable ID to its Ensembl ID, genomic location, biotype, and transcript list, fetch the DNA, cDNA, CDS, or protein sequence for a gene, transcript, protein, or genomic region, and find genomic features (genes, transcripts, variants, regulatory elements, exons) overlapping a chromosomal region.

The 7 tools it gives your agent

Extracted from the project's README - what ensembl-mcp-server lets an agent do.

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

Latest releases

v0.5.0 · 2026-09-24

Bounded region and sequence output, stricter input checks · ensembl_query_region caps its feature list with max_results (default 100, 0 uncapped) and returns assemblyName (#17, #23) · ensembl_get_sequence returns…

v0.4.4 · 2026-09-19

mcp-ts-core 0.13.6 adoption · Tool calls tolerate minor argument mismatches - an unrecognized top-level key is dropped, a differently-cased spelling of a declared parameter is rewritten onto the real key, and a…

v0.4.3 · 2026-08-22

MCP SDK v2 maintenance · MCP 2026-07-28 support rejects undeclared top-level inputs and advertises error envelopes, JSON Schema 2020-12, and client-visible logging. · Public cache hints and an explicit stateless HTTP…

04 · Who maintains Ensembl MCP Server

ensembl-mcp-server is maintained by cyanheads. We track 137 MCP servers from cyanheads - 131 actively maintained, 1,856 combined GitHub stars, oldest repo from Dec 2024. Full record: all servers from cyanheads.

05 · Facts

repository: github.com/cyanheads/ensembl-mcp-server
category: database - ranked #59 of 174 actively-maintained database servers as of 2026-09-30.
release cadence: 7 releases in the last 90 days (latest 2026-09-24)
registry: io.github.cyanheads/ensembl-mcp-server (active, first published 2026-06-05 · 13 versions)
packages: npm:@cyanheads/ensembl-mcp-server · npm:@cyanheads/ensembl-mcp-server

06 · Ensembl MCP Server FAQ

Is Ensembl MCP Server still maintained?

Yes - as of 2026-09-30, its last commit was 2026-09-24 and it shipped 7 releases in the last 90 days. We re-verify nightly.

What can Ensembl MCP Server do?

With this server connected, an agent can list species supported by Ensembl with display name, common name, assembly, taxon ID, and division, resolve a gene by symbol + species or by stable ID to its Ensembl ID, genomic location, biotype, and transcript list, fetch the DNA, cDNA, CDS, or protein sequence for a gene, transcript, protein, or genomic region, and find genomic features (genes, transcripts, variants, regulatory elements, exons) overlapping a chromosomal region.

How do I install Ensembl MCP Server?

Run `npx -y @cyanheads/ensembl-mcp-server`. The README documents 2 environment variables (MCP_TRANSPORT_TYPE, MCP_LOG_LEVEL) to set first. Set MCP_TRANSPORT_TYPE, MCP_LOG_LEVEL before connecting. You can also paste the ready-made client config above.

Does Ensembl MCP Server require authentication?

No - the endpoint accepted our unauthenticated MCP initialize when probed on 2026-09-30; you can connect without credentials.

07 · Alternatives to Ensembl MCP Server

Alternatives to Ensembl MCP Server

Maintained database servers if Ensembl MCP Server isn't the fit.

Pairs well with

Servers that cover what Ensembl MCP Server doesn't - only shown when the pairing reason fits the companion.

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