Back to search
100
MCP live MCP 2026-07-28 http

ensembl-mcp-server

io.github.cyanheads/ensembl-mcp-server

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

Watch this dependency

Get before/after evidence when observed tools, schemas, authentication access, availability or the endpoint changes.

Inspect evidence and set up a watch Share public evidence report
Uptime
100.0%
4 direct probes · 30d
Response
1781ms
last probe
Tools
7
callable
Resources
9
readable
Prompts
1
available
Primary URL
https://ensembl.caseyjhand.com/mcp
Score: 100/100
Handshake verified by our own probe.
why this score
pass Answers the MCP handshake 50/50
The handshake and the list calls succeeded on the primary URL.
pass Lists tools, resources or prompts 30/30
7 tools, 9 resources, 1 prompts returned.
pass 3 or more catalogue items 10/10
17 items in total; 3 or more earns these points.
pass Describes itself 10/10
99 characters; more than 30 earns these points.

Tools · 7

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 i…

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 …

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, molecu…

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 th…

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…

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 identi…

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 descript…

Resources · 9

Ensembl Species

Ensembl species catalog for the endpoint default division — internal name, display name, assembly, taxon ID, and division. On the default GRCh38 endpoint this is the vertebrate division (~356 species)…

ensembl://species
BRCA2 (homo_sapiens)

Example: BRCA2 breast cancer susceptibility gene

ensembl://gene/ENSG00000139618
TP53 (homo_sapiens)

Example: Tumor protein p53

ensembl://gene/ENSG00000141510
BRCA2-201 canonical transcript (homo_sapiens)

Example: canonical BRCA2 transcript

ensembl://transcript/ENST00000380152
EnsemblVertebrates species

Ensembl-supported species in the EnsemblVertebrates division

ensembl://species/EnsemblVertebrates
EnsemblPlants species

Ensembl-supported species in the EnsemblPlants division

ensembl://species/EnsemblPlants
EnsemblFungi species

Ensembl-supported species in the EnsemblFungi division

ensembl://species/EnsemblFungi
EnsemblMetazoa species

Ensembl-supported species in the EnsemblMetazoa division

ensembl://species/EnsemblMetazoa
EnsemblProtists species

Ensembl-supported species in the EnsemblProtists division

ensembl://species/EnsemblProtists

Prompts · 1

ensembl_gene_dossier

Structured research workflow for assembling a complete gene profile. Guides the agent through the Ensembl tool chain in order: symbol → ID + location → protein sequence → key variants → cross-species …

How to use

Add to your Claude Desktop / Cursor / Cline MCP config:

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