Ensembl MCP server

by cyanheads·io.github.cyanheads/ensembl-mcp-server·v0.4.3

Look up genes, sequences, variants, homologs, and cross-database xrefs from Ensembl REST.

What users say

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Safety scan

not scanned yet

Adoption

Not measured yet

Usage numbers are collected on the next scan

Reviews

Nobody has reviewed Ensembl yet.

If you have run it, two minutes of your experience saves the next person an afternoon.

Tool list not cached yet. `describe` through the gateway fetches it live.

Not scanned yet. New registry listings are scanned within a day of import.

claude mcp add --transport http ensembl-mcp-server https://ensembl.caseyjhand.com/mcp

Is Ensembl MCP server safe?: Not known yet: the safety scan has not run. New listings are scanned within a few days.
How do I install Ensembl?: It runs remotely at ensembl.caseyjhand.com. Add it to Claude Code, Claude Desktop or Cursor with the snippets above, or call it through the mcp.market gateway without installing anything.
Does Ensembl need an API key?: No secret keys are declared. It reads 8 settings from the environment.
Is Ensembl maintained?: The latest release is v0.4.3.
Is Ensembl up?: 100% of our last 1 checks got an answer. We check remote servers about four times a day.
What can I use instead of Ensembl?: Servers from other publishers that do the same job: BioMCP-TS MCP server, MCP Toolbox for Databases MCP server and Neon MCP server. Compare all Ensembl alternatives.

Same job from other publishers: the closest match first, then the best rated.

BioMCP-TS
Biomedical MCP server: genes, variants, trials, literature, patents, optional SQL/R/biowasm tools.
not reviewed
Growing
C
MCP Toolbox for Databases
MCP Toolbox for Databases enables your agent to connect to your database.
not reviewed
Established
A
Neon
Official Neon MCP server for managing Neon projects and Lakebase Postgres databases.
not reviewed
Established
A
Magic Cloud
Generate secured CRUD APIs over your database, run SQL, manage files, tasks and a headless browser
not reviewed
Established
A
Infrawise
Live AWS, database & Kafka infrastructure context for AI coding assistants via MCP.
not reviewed
Growing
A

With the gateway added, ask your agent for it by name:

agent prompt

call io.github.cyanheads/ensembl-mcp-server → <tool>

Free per call. Metered, capped by your key, logged for reliability.

ENSEMBL_BASE_URLEnsembl REST API base URL. Override to use GRCh37 endpoint or a local mirror.
MCP_LOG_LEVELSets the minimum log level for output (e.g., 'debug', 'info', 'warn').
ENSEMBL_BASE_URLEnsembl REST API base URL. Override to use GRCh37 endpoint or a local mirror.
MCP_HTTP_HOSTThe hostname for the HTTP server.
MCP_HTTP_PORTThe port to run the HTTP server on.
MCP_HTTP_ENDPOINT_PATHThe endpoint path for the MCP server.
MCP_AUTH_MODEAuthentication mode to use: 'none', 'jwt', or 'oauth'.
MCP_LOG_LEVELSets the minimum log level for output (e.g., 'debug', 'info', 'warn').

https://ensembl.caseyjhand.com/mcp

streamable-http

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Shows the safety grade and links back to this page. It updates itself after every scan and review.

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