Ensembl Connector for AI agents.

27 live capabilities

Query genomic sequences and gene trees directly from the Ensembl database.

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AI Agent

Why people use Ensembl

Ensembl for Faster Genomic Data Retrieval

With this Connector, you just describe what you need to your AI client. Instead of searching for a gene and then writing a script to find its orthologues, you ask for the orthologues directly. The agent handles the API calls and returns the data you need, letting you stay focused on the science.

What Vinkius changes

You get direct, conversational access to the Ensembl database without writing any code.

Use it from Claude, ChatGPT, Cursor or another AI client you already have.

One account · 5,900+ Connectors

Real-world use case 01

Comparative Genomics Analysis

A researcher asks their agent to find all orthologues for a human gene in mouse.
Real-world use case 02

Variant Impact Assessment

A clinician needs to know the effect of a specific rsID.
Real-world use case 03

Cross-Assembly Mapping

A scientist is moving data from an old genome build to a new one.

Complete set · 27capabilities

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.

01 Capability
Get info assembly
Lists the available assemblies and chromosomes for a species. This helps you understand the structural layout of a genome.
02 Capability
Get info rest
Shows the current version of the Ensembl REST API. Use this to check for the latest updates to the service.
03 Capability
Get info species
Lists all available species and their metadata. This is the best way to see what organisms are in the database.
04 Capability
Get vep id
Fetches consequences for a variant identifier like an rsID. This is the easiest way to check a known SNP's impact.

Capability set02 / 07

05—08

4 capabilities in this set.

Part of 27 available through Ensembl.

05 Capability
Get xrefs id
Retrieves external references for an Ensembl identifier. This helps you link your data to other major databases.
06 Capability
Get xrefs symbol
Looks up an external symbol and returns linked Ensembl objects. Use this to find the correct Ensembl ID from a common gene name.
07 Capability
Get alignment
Retrieves genomic alignments for a specific region. This helps you see how sequences line up across different species.
08 Capability
Get archive bulk
Returns the latest versions for a group of identifiers. Use this to quickly update a large list of gene IDs.

Capability set03 / 07

09—12

4 capabilities in this set.

Part of 27 available through Ensembl.

09 Capability
Get archive id
Finds the latest version of a single identifier. This ensures you're always working with the most current data.
10 Capability
Get ga4gh beacon
Provides allele information through a beacon service. This is great for checking specific genetic markers.
11 Capability
Search ga4gh variants
Searches for variants using the GA4GH schema. Use this to query specific genetic variations in your research.
12 Capability
Get genetree
Retrieves a gene tree for a stable identifier. It helps you visualize the evolutionary relationships of a gene.

Capability set04 / 07

13—16

4 capabilities in this set.

Part of 27 available through Ensembl.

13 Capability
Get homology
Pulls homology information by species and gene ID. Use this to find orthologs and paralogs across different organisms.
14 Capability
Get ld
Computes Linkage Disequilibrium values. This is essential for understanding how genetic markers are inherited together.
15 Capability
Get lookup bulk
Performs a bulk lookup for multiple identifiers. Use this to quickly find the database and species for a list of IDs.
16 Capability
Get lookup id
Finds the species and database for a single identifier. This is helpful when you have an ID but don't know its origin.

Capability set05 / 07

17—20

4 capabilities in this set.

Part of 27 available through Ensembl.

17 Capability
Get map cdna
Converts cDNA coordinates to genomic coordinates. This helps you translate transcript data into genome locations.
18 Capability
Get map
Converts coordinates from one assembly version to another. This is a lifesaver when moving between older and newer genome versions.
19 Capability
Get ontology id
Searches for an ontological term by its identifier. Use this to link your data to standard biological terms.
20 Capability
Get overlap region
Retrieves features that overlap a specific region. This helps you see what genes or markers are in a specific area.

Capability set06 / 07

21—24

4 capabilities in this set.

Part of 27 available through Ensembl.

21 Capability
Ping
Checks if the service is currently alive. Use this to verify your connection to the Ensembl API.
22 Capability
Get sequence id
Requests a sequence by its stable identifier. This gives you the raw data for a specific gene or transcript.
23 Capability
Get sequence region
Requests a genomic sequence by a specific region. Use this to pull a specific piece of DNA for analysis.
24 Capability
Get taxonomy id
Searches for a taxonomic term by ID or name. This helps you categorize species and organisms correctly.

Capability set07 / 07

25—27

3 capabilities in this set.

Part of 27 available through Ensembl.

25 Capability
Get variation
Retrieves variant features, genotypes, and population data. Use this to see how specific mutations occur in populations.
26 Capability
Get vep bulk
Provides consequence predictions for multiple regions. This is the fastest way to see the impact of several variants at once.
27 Capability
Get vep hgvs
Fetches consequences for a variant in HGVS notation. Use this when you need to understand a specific mutation's effect.

Set up in minutes

One URL. Then ask Ensembl to work.

Claude and ChatGPT only need the Connector URL. Copy it once, add it in settings, and use Ensembl from the conversation.

Choose your client

Live preview

Advanced clients IDE · CLI

Claude · Web + desktop

Official guide ↗

Connector URL · ready to paste

Streamable HTTP

https://edge.vinkius.com/vk_preview_m0hayIErvjxLYR70lCwlpWpppEzV8unFkuPlELTW/mcp

Step 01

Open Connectors

In Claude Web or Claude Desktop, open Settings and choose Connectors.
Step 02

Add the URL

Choose Add custom connector, name it Ensembl, and paste the URL above.
Step 03

Turn it on in chat

Select +, open Connectors, and enable Ensembl for the conversation.

ChatGPT · Web + desktop

Official guide ↗

Connector URL · ready to paste

Streamable HTTP

https://edge.vinkius.com/vk_preview_m0hayIErvjxLYR70lCwlpWpppEzV8unFkuPlELTW/mcp

Step 01

Open MCP settings

On desktop, open Settings and MCP servers. On web, open your workspace app or connector settings.
Step 02

Add the URL

Choose Add server with Streamable HTTP, or create a custom MCP app, then paste the Ensembl URL.
Step 03

Save and start

Save the connection and enable Ensembl in your conversation. Desktop may ask you to restart once.

Cursor · IDE configuration

Official guide ↗

Advanced setup

{
  "mcpServers": {
    "ensembl": {
      "url": "https://edge.vinkius.com/vk_preview_m0hayIErvjxLYR70lCwlpWpppEzV8unFkuPlELTW/mcp"
    }
  }
}

Step 01

Open MCP Settings

Press Cmd+Shift+P (macOS) or Ctrl+Shift+P (Windows/Linux) → search "MCP Settings"
Step 02

Add the server config

Paste the JSON configuration above into the mcp.json file that opens
Step 03

Save the file

Cursor will automatically detect the new Connector
Step 04

Start using Ensembl

Open Agent mode in chat and ask: "Using Ensembl, help me...". 27 tools available

VS Code Copilot · IDE configuration

Official guide ↗

Advanced setup

{
  "mcpServers": {
    "ensembl": {
      "url": "https://edge.vinkius.com/vk_preview_m0hayIErvjxLYR70lCwlpWpppEzV8unFkuPlELTW/mcp"
    }
  }
}

Step 01

Create MCP config

Create a .vscode/mcp.json file in your project root
Step 02

Add the server config

Paste the JSON configuration above
Step 03

Enable Agent mode

Open GitHub Copilot Chat and switch to Agent mode using the dropdown
Step 04

Start using Ensembl

Ask Copilot: "Using Ensembl, help me...". 27 tools available

Windsurf · IDE configuration

Official guide ↗

Advanced setup

{
  "mcpServers": {
    "ensembl": {
      "url": "https://edge.vinkius.com/vk_preview_m0hayIErvjxLYR70lCwlpWpppEzV8unFkuPlELTW/mcp"
    }
  }
}

Step 01

Open MCP Settings

Go to Settings → MCP Configuration or press Cmd+Shift+P and search "MCP"
Step 02

Add the server

Paste the JSON configuration above into mcp_config.json
Step 03

Save and reload

Windsurf will detect the new server automatically
Step 04

Start using Ensembl

Open Cascade and ask: "Using Ensembl, help me...". 27 tools available

Cline · IDE configuration

Official guide ↗

Advanced setup

{
  "mcpServers": {
    "ensembl": {
      "url": "https://edge.vinkius.com/vk_preview_m0hayIErvjxLYR70lCwlpWpppEzV8unFkuPlELTW/mcp"
    }
  }
}

Step 01

Open Cline MCP Settings

Click the Connectors icon in the Cline sidebar panel
Step 02

Add remote server

Click "Add Connector" and paste the configuration above
Step 03

Enable the server

Toggle the server switch to ON
Step 04

Start using Ensembl

Ask Cline: "Using Ensembl, help me...". 27 tools available

Claude Code · Terminal command

Official guide ↗

Advanced setup

claude mcp add ensembl --transport http "https://edge.vinkius.com/vk_preview_m0hayIErvjxLYR70lCwlpWpppEzV8unFkuPlELTW/mcp"

Step 01

Install Claude Code

Run npm install -g @anthropic-ai/claude-code if not already installed
Step 02

Add the Connector

Run the command above in your terminal
Step 03

Verify the connection

Run claude mcp to list connected servers, or type /mcp inside a session
Step 04

Start using Ensembl

Ask Claude: "Using Ensembl, show me...". 27 tools are ready

Where the request belongs

Work Ensembl can move forward.

Built around the request

This is for bioinformaticians and genomic researchers who are tired of manual data scraping. If you spend your day copying IDs between spreadsheets and web browsers, this capability is for you.

01

Bioinformatician

Uses the Connector to pull large batches of homology data for comparative genomics without writing custom R or Python scripts.

02

Genomic Researcher

Verifies stable identifiers and pulls variant effect predictions during literature reviews or experimental design.

03

Data Scientist

Automates the retrieval of genomic sequences and metadata for large-scale biological analysis and machine learning.

Build the capability set

Each Connector adds new actions and data without changing how you work.

Browse Connectors

01 4 capabilities

GenBank/NCBI API

Access genomic data. audit sequences, proteins, and UIDs via IA.

02 16 capabilities

EBI InterPro

Classify protein sequences into families, predict functional domains, and explore evolutionary relationships across species.

03 16 capabilities

EBI Proteins API

Query the UniProt knowledge base for protein sequences, annotations, and functional data across millions of characterized entries.

04 7 capabilities

KEGG

Access the Kyoto Encyclopedia of Genes and Genomes (KEGG) to query genomic, chemical, and systemic functional information directly from your AI agent.

05 3 capabilities

UniProt

Search 250M+ protein sequences with functional annotations, gene names, subcellular locations, and amino acid data from the world's most comprehensive protein knowledge base.

06 10 capabilities

Species

Access the GBIF Backbone Taxonomy to search, match, and explore species data, hierarchies, and biological media directly from your AI agent.

Bring your own AI

Change the model, client or framework. Keep Ensembl connected.

Before you connect

Questions about Ensembl.

The practical details behind the request, access and result.

Can the Ensembl MCP find orthologues for me?

Yes, it can find orthologues across different species. You can simply ask your agent to find the matches for a specific gene, and it will pull the homology data for you.

How do I get genomic sequences with Ensembl MCP?

You can request sequences by their stable identifier or by a specific region. Your agent will fetch the raw genomic data directly from the Ensembl database.

Can I use Ensembl MCP for variant analysis?

Yes, it provides access to variant effect prediction. You can ask about specific mutations to see how they impact biology or get consequences for a list of regions.

Does Ensembl MCP support multiple species?

It supports over 300 species. You can list the available species or query specific metadata for any of them through your AI client.

Can I map coordinates between different assemblies?

Yes, the Connector includes a capability to convert coordinates from one assembly version to another. This is very helpful when working with older and newer genome builds.

Is the Ensembl MCP good for large-scale data pulls?

It's great for bulk lookups. You can provide a list of identifiers, and the agent can retrieve the latest versions and metadata for all of them in one go.

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.

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).

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.

One connection away

Give your agent a direct line to Ensembl.

Connect Ensembl once. Keep it beside 5,900+ managed Connectors when the next task needs more.

Explore every Connector No credit card required · Free tier available