MCP server

Ensembl

io.github.cyanheads/ensembl-mcp-server

Checked 26 Oct 2026, 08:29 UTC · Connected to it and listed its tools

Look up genes, sequences, variants, homologs, and cross-database xrefs from Ensembl REST.

Source

At a glance

Type

MCP server

Publisher

Not verified

Status

Working at last check

Tools

7

Token cost

About 6,272 tokens per request

Sets up in

Claude Code, Claude Desktop, Codex, Gemini CLI, Cursor, VS Code, Antigravity, ChatGPT, OpenAI API, Grok

Last checked

26 Oct 2026, 08:29 UTC

Connect it to your agent

Add to CursorAdd to VS CodeVS Code Insiders

Opens the app, which shows the server and asks you to confirm. For other apps, copy the setup below.

Claude Code

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

Claude Desktop

Settings → Connectors → Add custom connector, and paste the URL.

Codex (config.toml)

[mcp_servers.ensembl-mcp-server]
url = "https://ensembl.caseyjhand.com/mcp"

Gemini CLI

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

Cursor

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

VS Code

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

Antigravity

agy mcp add ensembl-mcp-server https://ensembl.caseyjhand.com/mcp

ChatGPT

Settings → Apps & Connectors → Advanced settings: turn on Developer mode, then Create a connector and paste the URL. Which plans can do this varies.

OpenAI API (Responses tools)

{"type":"mcp","server_label":"ensembl-mcp-server","server_url":"https://ensembl.caseyjhand.com/mcp","require_approval":"always"}

Grok (xAI API tools)

{"type":"mcp","server_label":"ensembl-mcp-server","server_url":"https://ensembl.caseyjhand.com/mcp"}

Tools

• ensembl_get_homology ~767 tokens
  Find orthologs and/or paralogs of a gene across species. Returns each homolog's stable ID, species, homology type (ortholog_one2one, ortholog_one2many, paralog_many2many, etc.), percId (percent identity), percPos (percent positives), and taxonomy level. Essential for cross-species research — for exa
• ensembl_get_sequence ~1285 tokens
  Fetch the DNA, cDNA, CDS, or protein sequence for a gene, transcript, protein, or genomic region. Returns a window of the sequence — the first 10,000 characters by default — with its stable ID, molecule type, and full length. When more follows the window, truncated is true and nextOffset is the offs
• ensembl_get_xrefs ~597 tokens
  Retrieve cross-database references for a gene or feature — HGNC, UniProt, EntrezGene, OMIM, RefSeq, Reactome, and others. Returns each xref with its database name, primary ID, display ID, and description. By default only the requested object level is queried; all_levels=true includes transcript and
• ensembl_list_species ~613 tokens
  List species supported by Ensembl with display name, common name, assembly, taxon ID, and division. Required discovery step — species names like homo_sapiens are opaque to non-biologists and are the input format every other Ensembl tool expects. Use nameContains to find a species by partial name mat
• ensembl_lookup_gene ~1038 tokens
  Resolve a gene by symbol + species (or by stable ID) to its Ensembl ID, genomic location (chr:start-end:strand), biotype, description, and transcript list. Entry point for most workflows — the stable ID and coordinates returned here are inputs to other tools. Accepts both symbol lookup (BRCA2 + homo
• ensembl_predict_variant ~914 tokens
  Predict the functional consequences of a sequence variant using the Ensembl Variant Effect Predictor (VEP). Accepts three input formats: HGVS notation (transcript-relative, e.g. ENST00000380152.8:c.2T>A, or genomic, e.g. 13:g.32316462T>A); region+allele (chr:start:end:strand/allele, e.g. 1:65568:655
• ensembl_query_region ~1058 tokens
  Find genomic features overlapping a chromosomal region: genes, transcripts, variants, regulatory elements, or exons. Returns each feature with its stable ID, type, location, biotype, and name, plus the genome assembly the coordinates are on. Useful for "what's in this locus?" and for seeding follow-

Browse

• GitHub tools
• Website monitoring
• GitHub and code hosting
• Databases
• Translation

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