How to Use the Ensembl MCP in Claude

Q: How do I install the Ensembl MCP Server on Claude Desktop?

Open your local claudedesktopconfig.json file and add the Ensembl server under the mcpServers key with your Vinkius credentials. Restart your Claude Desktop app, and you will see the genomic tools ready to use via the hammer icon in your chat window.

Q: Can Claude Desktop handle bulk Ensembl lookups?

Yes, Claude Desktop uses the getlookupbulk tool to resolve multiple gene identifiers in a single round-trip. This prevents rate-limiting issues when processing large gene lists in your chat.

Q: How does Claude Desktop fetch homology data from Ensembl?

The agent calls gethomology with your target species and gene ID directly from the chat input. Claude Desktop then parses the taxonomic relationships and displays the orthologs or paralogs in a clean markdown table.

Pull gene trees, variant consequences, and alignments directly into Claude Desktop to run genomic lookups in your chat.

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Connect Ensembl MCP to Claude Desktop

Create your Vinkius account to connect Ensembl to Claude Desktop and route execution through our secure gateway. The platform manages server hosting, runtime updates, and security layers. Configuration requires no manual server provisioning.

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Setup Ensembl with Claude Desktop

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Run VEP variant predictions inside Claude Desktop

The `get_vep_id` and `get_vep_bulk` tools fetch variant consequences directly inside your Claude Desktop chat interface. You paste a list of rsIDs or genomic coordinates, and Claude Desktop parses the predicted functional impacts without you opening a separate web browser tab. We use the Vinkius managed MCP Server to pipe these Ensembl predictions straight to your local Claude Desktop app. If your analysis fails on a specific coordinate, you can immediately switch to `get_vep_hgvs` to check the HGVS notation and pinpoint the exact mutation details.

Map coordinate assemblies on the fly

The `get_map` tool converts genomic coordinates between assembly versions within your Claude Desktop conversational workspace. When you ask Claude Desktop to translate coordinates from GRCh37 to GRCh38, the agent calls this endpoint and updates your active research notes instantly. You can also call `get_info_assembly` to check which chromosomes are available for a specific species before running the conversion. This setup cuts out the manual liftover steps, leaving you with raw, verified coordinate mappings directly inside your Claude Desktop chat history.

Extract sequence alignments without leaving the chat

The `get_alignment` and `get_sequence_region` tools pull raw genomic sequences and comparative alignments into your Claude Desktop window. Your agent reads the exact nucleotide sequence for a specified region and formats it as plain text or FASTA format on your screen. This integration means you don't have to download multi-gigabyte files just to inspect a single promoter region. Claude Desktop queries the Ensembl API directly, retrieves the exact slice of DNA, and displays the alignment blocks for your comparative analysis.

Setup guide

Set up Ensembl MCP in Claude Web or Desktop

1

Open Claude Settings

Go to claude.ai, click your profile icon, then navigate to Customize → Connectors.
2

Add Custom Connector

Click the "+" button and select Add custom connector. Paste your Vinkius endpoint URL: https://edge.vinkius.com/[YOUR_TOKEN_HERE]/mcp Replace [YOUR_TOKEN_HERE] with your token from cloud.vinkius.com. For OAuth-protected servers, expand Advanced settings to add credentials.
3

Start a conversation

Open a new chat. The Ensembl MCP tools are available immediately — no restart needed.

Endpoint URL

https://edge.vinkius.com/[YOUR_TOKEN_HERE]/mcp

No configuration file needed — paste the URL directly in the Claude web interface.

Available on Free (1 connector), Pro, Max, Team, and Enterprise plans.

Prerequisites

Claude Desktop installed (macOS or Windows)
Active Vinkius subscription with a valid endpoint token

1

Open Claude Desktop Settings

Click the menu icon at the top-left corner, go to Settings → Developer → Edit Config. This opens claude_desktop_config.json in your default text editor.
2

Paste the Ensembl MCP configuration

Copy the JSON snippet on the right into the mcpServers object. Replace [YOUR_TOKEN_HERE] with your endpoint token from cloud.vinkius.com.
3

Restart Claude Desktop

Close and reopen the application. Claude needs a full restart to load new MCPs — refreshing a conversation is not enough.
4

Verify the connection

Open a new conversation. Click the 🔌 icon at the bottom of the message input. You should see tools listed under ensembl-mcp.

json

{
  "mcpServers": {
    "ensembl-mcp": {
      "url": "https://edge.vinkius.com/[YOUR_TOKEN_HERE]/mcp"
    }
  }
}

Get your connection token →

Independent Platform Disclaimer: Vinkius is an independent platform and is not affiliated with, endorsed by, sponsored by, verified by, or otherwise authorized by Ensembl. All third-party trademarks, logos, and brand names are the property of their respective owners. Their use on this website is strictly for informational purposes to identify service compatibility and interoperability.

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Common questions about Ensembl MCP in Claude Desktop

Open your local `claude_desktop_config.json` file and add the Ensembl server under the `mcpServers` key with your Vinkius credentials. Restart your Claude Desktop app, and you will see the genomic tools ready to use via the hammer icon in your chat window.

Yes, Claude Desktop uses the `get_lookup_bulk` tool to resolve multiple gene identifiers in a single round-trip. This prevents rate-limiting issues when processing large gene lists in your chat.

Yes, you can add the Ensembl MCP Server as a custom connector in your Claude Desktop browser settings. Paste your remote Vinkius URL, complete the connection, and your browser-based agent will gain immediate access to the genomic database.

The agent calls `get_homology` with your target species and gene ID directly from the chat input. Claude Desktop then parses the taxonomic relationships and displays the orthologs or paralogs in a clean markdown table.

Your genomic sequences, rsIDs, and coordinate queries pass through a secure, ephemeral Vinkius sandbox before reaching the Ensembl API. Vinkius does not store your target gene identifiers or sequence data, ensuring your proprietary research targets remain private.

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