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Use Ensembl with your AI.

Connect your account once and let the AI you already use work with it, without building another integration. Access genomic data, gene trees, homologies, and cross-references from the Ensembl database directly from any AI agent.

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MCP VERIFIED · PRODUCTION READY · VINKIUS GUARANTEED

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Works with modern AI clients that support MCP, including ChatGPT, Claude, Cursor, and more.

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Complete set · 27 capabilities

The complete Ensembl capability set.

These are the exact actions your AI can choose when you ask it to work with Ensembl.

Capability set01 / 07

01-04

4 capabilities in this set.

Part of 27 available through Ensembl.

  1. 01

    Get xrefs symbol

    Look up an external symbol and return linked Ensembl objects

  2. 02

    Get archive bulk

    Retrieve the latest version for a set of identifiers

  3. 03

    Get archive ID

    Returns the latest version of a given identifier

  4. 04

    Get ga4gh beacon

    Beacon service for allele information

Capability set02 / 07

05-08

4 capabilities in this set.

Part of 27 available through Ensembl.

  1. 05

    Get homology

    Retrieves homology information by species and gene ID

  2. 06

    Get ld

    Compute Linkage Disequilibrium (LD) values

  3. 07

    Get lookup bulk

    Bulk lookup for multiple identifiers

  4. 08

    Search ga4gh variants

    Search for variants using GA4GH schema

Capability set03 / 07

09-12

4 capabilities in this set.

Part of 27 available through Ensembl.

  1. 09

    Get lookup ID

    Find the species and database for a single identifier

  2. 10

    Get map cdna

    Convert cDNA coordinates to genomic coordinates

  3. 11

    Get ontology ID

    Search for an ontological term by its identifier

  4. 12

    Get overlap region

    ) overlapping a region. Retrieve features overlapping a specific region

Capability set04 / 07

13-16

4 capabilities in this set.

Part of 27 available through Ensembl.

  1. 13

    Ping

    Check if the service is alive

  2. 14

    Get taxonomy ID

    Search for a taxonomic term by ID or name

  3. 15

    Get variation

    Retrieve variant features, genotypes, and population data

  4. 16

    Get vep bulk

    Bulk consequence prediction for multiple regions

Capability set05 / 07

17-20

4 capabilities in this set.

Part of 27 available through Ensembl.

  1. 17

    Get vep hgvs

    Fetch consequences for a variant in HGVS notation

  2. 18

    Get alignment

    Retrieves genomic alignments for a specific region

  3. 19

    Get genetree

    Retrieves a gene tree for a stable identifier

  4. 20

    Get info assembly

    List available assemblies and chromosomes for a species

Capability set06 / 07

21-24

4 capabilities in this set.

Part of 27 available through Ensembl.

  1. 21

    Get info rest

    Current version of the Ensembl REST API

  2. 22

    Get info species

    Lists all available species and their metadata

  3. 23

    Get map

    Convert coordinates from one assembly version to another

  4. 24

    Get sequence ID

    Request sequence by stable identifier

Capability set07 / 07

25-27

3 capabilities in this set.

Part of 27 available through Ensembl.

  1. 25

    Get sequence region

    Request genomic sequence by region

  2. 26

    Get vep ID

    Fetch consequences for a variant identifier (e.g., rsID)

  3. 27

    Get xrefs ID

    Retrieve external references for an Ensembl identifier

Observed, not estimated

1055ms average. Fast in production.

Ensembl is checked daily against the live service.

Daily averagePeak 1206ms
Aug 20Today
Fastest day
866ms
Slowest day
1206ms
14-day trend
Slowing+16%

Connect your client

One URL. Every client.

Activate the Connector, copy your link, and paste it into the client you already use. 27 capabilities arrive ready to run.

Preview access · not provider authentication

The vk_preview_* token belongs to Vinkius preview infrastructure. It lets Claude discover and display the capabilities of Ensembl, so you can see the experience inside your AI.

It does not authenticate your account with Ensembl. Actions requiring credentials or live account data may not run until you activate the Connector and authorize the service.

Ensembl Connector

You're all set. Choose your MCP client and follow the setup instructions.

Connector linkhttps://edge.vinkius.com/vk_preview_m0hayIErvjxLYR70lCwlpWpppEzV8unFkuPlELTW/mcp

Claude Desktop

Follow the steps below to connect in seconds.

  1. 1In Claude Desktop, open Settings → Connectors.
  2. 2Click “Add custom connector” and paste the connector link above as the remote MCP server URL.
  3. 3Click Add and start a new chat — Ensembl capabilities are ready to use.
Configuration · claude_desktop_config.jsonCopy
{
  "mcpServers": {
    "ensembl-mcp": {
      "url": "https://edge.vinkius.com/vk_preview_m0hayIErvjxLYR70lCwlpWpppEzV8unFkuPlELTW/mcp"
    }
  }
}
  • Claude
  • ChatGPT
  • Cursor
  • VS Code
  • Windsurf
  • Claude Code
  • JetBrains
  • Cline

Step-by-step instructions for each client are in the guide. How to connect

FAQ

Questions Ensembl owners ask.

  • 01

    How can I find orthologs for a specific gene across different species?

    Use the get_homology capability by providing the species name and the Ensembl gene ID. You can filter by type (e.g., 'orthologues') to see related genes in other organisms.

  • 02

    Can I retrieve the evolutionary gene tree for a specific identifier?

    Yes! The get_genetree capability allows you to fetch the gene tree for any stable Ensembl ID, with options for alignment and sequence types (protein or cdna).

  • 03

    How do I map a common gene symbol like 'BRCA2' to its Ensembl ID?

    Use the get_xrefs_symbol capability. Provide the species (e.g., 'human') and the symbol 'BRCA2' to retrieve all linked Ensembl objects and their stable identifiers.

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