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Connect Ensembl to ChatGPT, Claude and Gemini

Set it up once and it works in ChatGPT, Claude, Cursor, and any other client you love. It all runs safely in the background, so you can relax and focus on what really matters. Pull biological data and gene sequences through natural conversation.

Ask AI about this Connector

Developed, maintained, and hosted by Vinkius.

MCP VERIFIED · PRODUCTION READY · VINKIUS GUARANTEED

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

ChatGPTClaudeCursorPerplexityGeminiMicrosoft CopilotRaycastMeta AI

Your AI does the work. We keep it safe and sound.

No other AI tool gives you this. Your workflow runs in the client you already love, your account stays protected, and you decide what the agent can and cannot do. It is the whole reason to make the switch.

Each Connector lives inside our infrastructure, the same place where your workflow runs. The three things below are already part of it, working quietly in the background so you never have to think about them. Nothing to add, nothing to set up, nothing to worry about.

A futuristic MCP client docking bay
V8 Isolate01

Each Connector runs inside its own sealed environment.

Each Connector runs inside its own sealed V8 runtime — no access to your files, your system, or other servers. A Connector never sees past its own request.

Kill Switch02

One switch stops every agent. Instantly.

One action deactivates every Connector, revokes every token, and ends every session at once. AI Governance keeps the record.

FinOps per User03

Spending limits that pause instead of surprise.

Every user keeps their own connections and credentials, isolated from everyone else. Anything that would cross your spending limit is held for your approval, not billed.

Three controls, built into the layer your AI connects through.

Curated set · 27 capabilities

We ship only the actions that matter.

Capability set01 / 07

01-04

4 capabilities in this set.

Part of 27 available through Ensembl.

  1. 01

    Get xrefs symbol

    This capability looks up an external symbol to find its linked Ensembl objects.

  2. 02

    Get archive bulk

    Use this to grab the latest version for a specific set of identifiers.

  3. 03

    Get archive ID

    This capability returns the most recent version of a single identifier.

  4. 04

    Get ga4gh beacon

    Access the Beacon service to retrieve allele information.

Capability set02 / 07

05-08

4 capabilities in this set.

Part of 27 available through Ensembl.

  1. 05

    Get homology

    This capability pulls homology data using a species name and a gene ID.

  2. 06

    Get ld

    Use this to calculate Linkage Disequilibrium values.

  3. 07

    Get lookup bulk

    This capability performs a bulk lookup for multiple identifiers at once.

  4. 08

    Search ga4gh variants

    Search for specific variants using the GA4GH schema.

Capability set03 / 07

09-12

4 capabilities in this set.

Part of 27 available through Ensembl.

  1. 09

    Get lookup ID

    This capability identifies the species and database associated with a single identifier.

  2. 10

    Get map cdna

    Convert cDNA coordinates into genomic coordinates.

  3. 11

    Get ontology ID

    Search for an ontological term by its specific identifier.

  4. 12

    Get overlap region

    This capability finds features that overlap a specific genomic region.

Capability set04 / 07

13-16

4 capabilities in this set.

Part of 27 available through Ensembl.

  1. 13

    Ping

    Check if the Ensembl service is currently active.

  2. 14

    Get taxonomy ID

    Find a taxonomic term using its name or ID.

  3. 15

    Get variation

    Retrieve data on variant features, genotypes, and populations.

  4. 16

    Get vep bulk

    Perform bulk consequence predictions for several regions.

Capability set05 / 07

17-20

4 capabilities in this set.

Part of 27 available through Ensembl.

  1. 17

    Get vep hgvs

    Get consequences for a variant described in HGVS notation.

  2. 18

    Get alignment

    This capability retrieves genomic alignments for a designated region.

  3. 19

    Get genetree

    Pull a gene tree for a specific stable identifier.

  4. 20

    Get info assembly

    List the chromosomes and assemblies available for a species.

Capability set06 / 07

21-24

4 capabilities in this set.

Part of 27 available through Ensembl.

  1. 21

    Get info rest

    Check the current version of the Ensembl REST API.

  2. 22

    Get info species

    Retrieve a list of all available species and their metadata.

  3. 23

    Get map

    Convert coordinates between different assembly versions.

  4. 24

    Get sequence ID

    Request a genomic sequence using a stable identifier.

Capability set07 / 07

25-27

3 capabilities in this set.

Part of 27 available through Ensembl.

  1. 25

    Get sequence region

    Get a genomic sequence for a specific region.

  2. 26

    Get vep ID

    Fetch consequences for a specific variant identifier like an rsID.

  3. 27

    Get xrefs ID

    Retrieve external references linked to an Ensembl identifier.

Real work

What teams actually run

01

Orthologue Identification

Find equivalent genes in different species to study evolutionary conservation.

02

Variant Analysis

Predict the biological impact of a mutation using VEP capabilities.

03

Data Normalization

Convert genomic coordinates between different assembly versions to maintain consistency.

04

Database Cross-Referencing

Link Ensembl identifiers to external databases using symbols or IDs.

Automate a task

Put Ensembl to work on one thing.

Step-by-step automations your AI runs through this Connector: the workflow, the prompts to start with, and the exact capabilities behind each move.

One connector, every AI

Ensembl works with the most popular AI clients.

These are the most popular clients, each with a step-by-step guide: one link, set up once, with governance and visibility built in. And because everything runs on the MCP standard, the same connection also works in any other compatible client — nothing to rebuild.

ClaudeClaudeChatGPTChatGPTGeminiGeminiPerplexityPerplexityGrokGrokMicrosoft CopilotMicrosoft CopilotCursorCursorVS CodeVS CodeWindsurfWindsurfJetBrainsJetBrainsClineClineLangChainLangChainVercel AI SDKVercel AI SDKLovableLovableZ.aiZ.aiRaycastRaycastQwen CodeQwen CodeKimi CodeKimi CodeLe ChatLe Chat

Building your own app? The connector is yours to use.

You don't need a client to put Ensembl to work: the same hosted connection plugs into your own applications and agent code, with the same governance on every request. Build with it, chat with it — one connection for both.

Observed, not estimated

1128ms average. Fast in production.

Ensembl is checked daily against the live service.

Daily averagePeak 1398ms
Oct 3Today
Fastest day
913ms
Slowest day
1398ms
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

Guided setup for Claude? Set up Ensembl in Claude and other AIs

See all the AI clients this connector works with ↑

Who it's for

Built for the work Ensembl owners hand off.

This MCP is built for researchers working with large-scale biological datasets who want to bypass manual coding for routine queries.

  • 01

    Bioinformaticians

    They use the MCP to pull gene trees and homology data instead of writing custom Python or R scripts.

  • 02

    Genomic Researchers

    They use the capability to verify stable ID versions and cross-reference symbols within their research environment.

  • 03

    Data Scientists

    They automate the retrieval of genomic alignments and metadata for large-scale biological analysis.

FAQ

Questions Ensembl owners ask.

  • 01

    Do I need to write code to use this MCP?

    No. You interact with the Ensembl database using natural language through your AI client.

  • 02

    Can I use this with Claude or Cursor?

    Yes. This MCP is compatible with any MCP-enabled client, including Claude, Cursor, and Windsurf.

  • 03

    How do I access the public Ensembl data?

    When setting up your configuration, simply use 'PUBLIC' for standard access to the Ensembl REST API.

  • 04

    What kind of genomic sequences can I get?

    You can request sequences using specific stable identifiers or by defining a genomic region.

  • 05

    Does this support variant prediction?

    Yes. The MCP includes capabilities for bulk consequence prediction and specific HGVS notation queries.

  • 06

    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.

  • 07

    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).

  • 08

    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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