Click on "Install Server".
Wait a few minutes for the server to deploy. Once ready, it will show a "Started" state.
In the chat, type @ followed by the MCP server name and your instructions, e.g., "@mcp-ensembl look up the gene TP53 in human"
That's it! The server will respond to your query, and you can continue using it as needed.
Here is a step-by-step guide with screenshots.
Ensembl REST MCP.
Part of Pipeworx — an MCP gateway connecting AI agents to 673+ live data sources.
Tool | Description |
| Lookup by stable id (gene/transcript/exon/translation). |
| Gene by symbol within a species. |
| External cross-references for a gene symbol. |
| Sequence by stable id. |
| Homology mappings for a gene. |
| Variation record by name. |
| Variant Effect Predictor — region in "chrom:start-end:strand" form. |
Related MCP server: Ensembl MCP Server
Add to your MCP client (Claude Desktop, Cursor, Windsurf, etc.):
{
"mcpServers": {
"ensembl": {
"url": "https://gateway.pipeworx.io/ensembl/mcp"
}
}
}Or connect to the full Pipeworx gateway for access to all 673+ data sources:
{
"mcpServers": {
"pipeworx": {
"url": "https://gateway.pipeworx.io/mcp"
}
}
}Instead of calling tools directly, you can ask questions in plain English:
ask_pipeworx({ question: "your question about Ensembl data" })The gateway picks the right tool and fills the arguments automatically.
MIT
This server cannot be installed
Unclaimed servers have limited discoverability.
If you are the server author, to access and configure the admin panel.
Look up genes, fetch sequences, predict variant consequences, find orthologs and xrefs via Ensembl.
PubMed MCP — wraps the NCBI E-utilities API (biomedical literature, free, no auth)
MyVariant.info MCP.
We provide all the information about MCP servers via our MCP API.
curl -X GET 'https://glama.ai/api/mcp/v1/servers/pipeworx-io/mcp-ensembl'
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