How to Use the Ensembl MCP in Cursor

Q: How do I configure the Ensembl MCP Server in my Cursor project?

Create a .cursor/mcp.json file in your repository root and add the Ensembl server configuration. Cursor will automatically detect the genomic tools and make them available to your Composer or Agent mode.

Q: Can Cursor run Ensembl homology searches during code generation?

Yes, the Cursor agent calls gethomology to pull real comparative genomics data into your workspace. This helps you write and test biological data structures using authentic evolutionary relationships.

Q: How does the Ensembl MCP Server handle coordinate liftovers in Cursor?

Cursor invokes the getmap tool to convert genomic coordinates between assembly versions like GRCh37 and GRCh38. The agent then writes the mapping logic directly into your active code file using the verified coordinates.

Q: Can I query Ensembl gene trees using Cursor?

Yes, you can ask Cursor to fetch a gene tree using the getgenetree tool. The agent retrieves the tree structure and formats it as a JSON object or visual tree diagram inside your editor sidebar.

Generate code using real Ensembl genomic data directly in Cursor during your active coding sessions.

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Connect Ensembl MCP to Cursor

Create your Vinkius account to connect Ensembl to Cursor 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 Cursor

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Generate bioinformatic scripts in Cursor with real data

The `get_sequence_id` tool fetches raw DNA or protein sequences directly into your Cursor editor. When writing python scripts to analyze genes, Cursor uses this tool to pull actual sequences instead of generating fake placeholder text. This means your test suites run against real Ensembl data from the start. Your Cursor agent writes the parsing logic, executes the tool to grab the sequence, and verifies that your code handles the actual genomic string format correctly.

Resolve gene identifiers while writing code

The `get_lookup_id` and `get_xrefs_symbol` tools map external gene symbols to stable Ensembl identifiers inside your Cursor editor. As you write database migration scripts or data pipelines, the editor queries the Ensembl MCP Server to verify that your target IDs exist. Your Cursor agent can also invoke `get_xrefs_id` to fetch linked external references for any given gene. This prevents database foreign key failures by verifying biological identifiers before you run your pipeline code.

Annotate variant files directly in your Cursor terminal

The `get_vep_bulk` tool calculates variant consequences for large coordinate batches within the Cursor agent workspace. When debugging a pipeline that processes VCF files, Cursor calls this endpoint to predict variant effects on the fly. You can inspect predicted consequences for multiple regions without leaving your active Cursor codebase. The Cursor agent uses the returned JSON payload to write and test your custom variant filtering algorithms on actual Ensembl genomic data.

Setup guide

Set up Ensembl MCP in Cursor

Prerequisites

Cursor installed (macOS, Windows, or Linux)
Active Vinkius subscription with a valid endpoint token

1

Open MCP Settings

Go to Cursor Settings → MCP or open the Command Palette (Cmd+Shift+P / Ctrl+Shift+P) and search for "MCP: Add Server".
2

Add the Ensembl MCP

Cursor will create or open .cursor/mcp.json in your project root. Paste the JSON snippet on the right. Replace [YOUR_TOKEN_HERE] with your endpoint token from cloud.vinkius.com.
3

Enable Agent mode

Open Composer (Cmd+I / Ctrl+I) and switch to Agent mode using the dropdown at the top. MCP tools are only available in Agent mode.
4

Verify the connection

Ask Cursor something like "List my recent Ensembl transactions." If the MCP tools are loaded correctly, Cursor will call the Ensembl tools automatically. You can also check Settings → MCP for a green status indicator.

.cursor/mcp.json

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

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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 Cursor

Create a `.cursor/mcp.json` file in your repository root and add the Ensembl server configuration. Cursor will automatically detect the genomic tools and make them available to your Composer or Agent mode.

Yes, the Cursor agent calls `get_homology` to pull real comparative genomics data into your workspace. This helps you write and test biological data structures using authentic evolutionary relationships.

Cursor invokes the `get_map` tool to convert genomic coordinates between assembly versions like GRCh37 and GRCh38. The agent then writes the mapping logic directly into your active code file using the verified coordinates.

Yes, you can ask Cursor to fetch a gene tree using the `get_genetree` tool. The agent retrieves the tree structure and formats it as a JSON object or visual tree diagram inside your editor sidebar.

All variant IDs, genomic coordinates, and gene queries processed by Cursor are routed through the MCP Server's isolated V8 sandbox. Vinkius secures this data in transit and never caches your genomic targets, keeping your drug discovery pipelines confidential.

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