Ensembl MCP server
online · 100% uptimeLook up genes, sequences, variants, homologs, and cross-database xrefs from Ensembl REST.
not scanned yet
3 stars664 downloads/wk
Reviews
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If you have run it, two minutes of your experience saves the next person an afternoon.
Ensembl tools
Tool list not cached yet. `describe` through the gateway fetches it live.
How Ensembl compares
Against every graded Databases MCP server, from our own scans and uptime checks. Updated after each scan run.
- Safety score
- 93/100
- higher than 96% of 802 Databases servers
- Uptime
- 100%
- of our recent checks; the typical remote Databases server answers 100%
- Response time
- 229 ms
- faster than 52% of 292 Databases servers
- GitHub stars
- 3
- more than 65% of 602 Databases servers
- Downloads a week
- 664
- more than 86% of 328 Databases servers with a package
Release history: 9 versions in the registry since 2026-08-22, latest 2026-10-29, typically one every 5 days.
Install Ensembl in Claude Code, Cursor or VS Code
claude mcp add --transport http ensembl-mcp-server https://ensembl.caseyjhand.com/mcp
What the publisher says
From the Ensembl repository's README, as published. We do not edit it. Read it on GitHub
@cyanheads/ensembl-mcp-server Look up genes, fetch sequences, predict variant consequences, find orthologs, and retrieve cross-database xrefs from Ensembl REST via MCP. STDIO or Streamable HTTP. 7 Tools • 4 Resources • 1 Prompt
Public Hosted Server: https://ensembl.caseyjhand.com/mcp
Overview
Gene, sequence, and variant data for vertebrates and other model organisms from the Ensembl REST API. Look up genes, fetch sequences, predict variant consequences, find orthologs, and cross-reference external databases from any MCP client. Runs as a stdio process, a local Streamable HTTP server, or the public hosted endpoint above.
Tools
Resources
Shortened. The full README is on GitHub.
Nothing above is checked by us. What we check is on the safety report.
Ensembl: common questions
- Is Ensembl MCP server safe?
- Yes, by our scan: it is graded A (93/100). Read the Ensembl safety report
- How do I install Ensembl?
- It runs remotely at ensembl.caseyjhand.com. Add it to Claude Code, Cursor, VS Code or Claude Desktop 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 9 settings from the environment.
- Is Ensembl maintained?
- The last commit was 21 days ago (2026-10-13). The latest release is v0.7.1.
- Is Ensembl up?
- 100% of our last 28 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: Faucet MCP server, BioMCP-TS MCP server and legacy2mcp MCP server. Compare all Ensembl alternatives.
- How does Ensembl compare with other Databases MCP servers?
- safety score 93/100 (higher than 96% of 802 Databases servers); uptime 100% (of our recent checks; the typical remote Databases server answers 100%); response time 229 ms (faster than 52% of 292 Databases servers). Full comparison.
Alternatives to Ensembl
Same job from other publishers: the closest match first, then the best rated.
FaucetSQL database to MCP tools and REST API: PostgreSQL, MySQL, SQL Server, Oracle, SQLite, Snowflake.not reviewedEstablishedA- BioMCP-TSBiomedical MCP server: genes, variants, trials, literature, patents, optional SQL/R/biowasm tools.not reviewedGrowingB
- legacy2mcpTurn a legacy SOAP/WSDL, database, or REST API into a safe, typed, audit-logged MCP servernot reviewedGrowingA
- CogniCoreMemory, reflection and safety for AI agents. Hosted or local, no vector database.5.0(1)GrowingA
- DBHubToken-efficient database MCP server for PostgreSQL, MySQL, MariaDB, SQL Server, Oracle, SQLitenot reviewedWidely usedA
