Ensembl Mcp Server

Connect Remote server

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

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

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

Settings > Connectors > Add custom connector
URL: https://ensembl.caseyjhand.com/mcp

Tools 7 found in our last check

• 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 specie…

• 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…

• 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 n…

• 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?" an…

• 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/all…

• 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 and percPos (percent identical and positive positions, over the target protein's length), and…

• 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, plus how Ensembl assigned it (infoType, infoText) and its evidence codes (…

Details

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  Pre-launch checks for AI-built apps: leaked keys, Supabase RLS gaps, browser-exposed env vars.

• Imf Mcp Server

  Query IMF SDMX 3.0 macroeconomic dataflows — WEO, BOP, CPI, exchange rates, 190 countries.

• Apex DB

  Vehicle specifications, emissions, and powertrain data with source provenance.

• TrialBase DB

  Clinical trials across multiple registries with identifiers and source links.

• PatchLabs

  Security checks for AI-built apps (Lovable, Supabase, Bolt): RLS, headers, monitoring, fixes.

• Tidy Byte Tools API

  Remote MCP for JSON repair, hashing, formatting, IDs, dates, units, and other small tools.