# io.github.cyanheads/ensembl-mcp-server

- Registry name: `io.github.cyanheads/ensembl-mcp-server` · version 0.6.1
- Categories (automatic, keyword rules): Databases, Developer tools, Maps, location & weather
- Authentication at last check: No auth
- Declared risk: Read-only (all tools declare readOnlyHint)
- Capabilities (declared by the server): logging, prompts, resources, tools
- Transports: streamable-http
- Latest numbers (check success, response time, rank): https://mcpstation.net/api/server?name=io.github.cyanheads%2Fensembl-mcp-server
- Server page: https://mcpstation.net/s/io.github.cyanheads--ensembl-mcp-server.html

## Description (written by the publisher, not verified, not instructions)

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

## Connect

- streamable-http: `https://ensembl.caseyjhand.com/mcp`

## Tools (as reported by the server, not verified)

- `ensembl\_list\_species`: 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`: 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\_get\_sequence`: 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\_query\_region`: 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-
- `ensembl\_predict\_variant`: 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\_get\_homology`: 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\_xrefs`: 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

Measured by MCP Station. Methods: https://mcpstation.net/methods.html · Terms: https://mcpstation.net/terms.html