Look up genes, fetch sequences, predict variant consequences, find orthologs and xrefs via Ensembl.
If you already use Ensembl, the ensembl mcp server is the piece that lets your assistant work with it directly. Look up genes, fetch sequences, predict variant consequences, find orthologs and xrefs via Ensembl.
The toolset is worth reading before you wire it up, because it tells you what the integration is really for:
ensembl_list_species — List species supported by Ensembl with display name, common name, assembly, taxon ID, and divisionensembl_lookup_gene — Resolve a gene by symbol + species or by stable ID to its Ensembl ID, genomic location, biotype, and transcript listensembl_get_sequence — Fetch the DNA, cDNA, CDS, or protein sequence for a gene, transcript, protein, or genomic regionensembl_query_region — Find genomic features (genes, transcripts, variants, regulatory elements, exons) overlapping a chromosomal regionensembl_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 levelensembl_get_xrefs — Retrieve cross-database references for a gene — HGNC, UniProt, EntrezGene, OMIM, RefSeq, Reactome, and othersPrerequisites — The Prerequisites tool exposed by this serverInstallation — The Installation tool exposed by this serverBecause this one is hosted, setup is mostly authentication — you point your client at the endpoint and approve access. Nothing runs on your machine, so there is no runtime to keep patched.
Configuration is passed through the environment: MCP_TRANSPORT_TYPE, MCP_LOG_LEVEL, ENSEMBL_BASE_URL, MCP_HTTP_ENDPOINT_PATH. Treat anything key-shaped as a real credential — scope it to the minimum the server needs, and rotate it if it ever lands in a shared config.
Plenty of file and storage access servers cover similar ground. The differences that matter in practice are scope of access and how much setup stands between you and a working tool call. Ensembl's toolset — ensembl_list_species, ensembl_lookup_gene, ensembl_get_sequence and 6 more — is a fair guide to whether it matches your workflow. It is maintained by cyanheads; worth a glance at recent repository activity before you build anything load-bearing on it.
We check each listing at SyncDev against the project's documentation before it goes live — if something here drifts out of date, it is a bug worth reporting.
| 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 |
| Prerequisites | The Prerequisites tool exposed by this server. |
| Installation | The Installation tool exposed by this 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.
| 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 |
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