The Ensembl MCP Server MCP server,
connected in one click.
Look up genes, sequences, variants, homologs, and cross-database xrefs from Ensembl REST. Connect the official Ensembl MCP Server MCP server to Claude, ChatGPT, or Cursor through gate — one gateway URL, no config files, security-checked.
Free to start · No credit card · No hosting needed
Add Ensembl MCP Server to your AI in one minute
Pick your client. Copy, paste, done — or let gate handle sign-ins and policies for you.
claude mcp add --transport http ensembl-mcp-server https://ensembl.caseyjhand.com/mcpRun in your terminal, then restart Claude Code.
Ensembl MCP Server · https://ensembl.caseyjhand.com/mcp
What your AI can do with Ensembl MCP Server
Real prompts you can type the moment it's connected — no setup, no docs to read.
“Use “ensembl_list_species”: List species supported by Ensembl with display name, common name, assembly, taxon ID, and division. Required discovery step — species names.”
“Use “ensembl_lookup_gene”: Resolve a gene by symbol + species (or by stable ID) to its Ensembl ID, genomic location (chr:start-end:strand), biotype, description, and t.”
“Use “ensembl_get_sequence”: Fetch the DNA, cDNA, CDS, or protein sequence for a gene, transcript, protein, or genomic region. Returns the sequence with its stable ID, m.”
“Use “ensembl_query_region”: Find genomic features overlapping a chromosomal region: genes, transcripts, variants, regulatory elements, or exons. Returns each feature wi.”
How secure is the Ensembl MCP Server MCP server?
Every server in the gate directory has to pass the same four checks before your AI can touch it. Here's how Ensembl MCP Server holds up.
Security grade A
gate scanned 7 tools on Sep 26, 2026 for prompt injection and risky tool definitions — nothing to flag.
- lowensembl_get_sequence: Unusually long tool description
- lowensembl_query_region: Unusually long tool description
- lowensembl_predict_variant: Unusually long tool description
Official endpoint
Operated by Ensembl MCP Server (caseyjhand.com) at its documented MCP endpoint — not a third-party mirror or community re-host.
No sign-in needed
This server only exposes public data — no account and no credentials are involved when you connect.
Scanned before it goes live
gate checks every tool for prompt injection, hidden instructions, data-exfiltration hints, and over-broad permissions before the server is available through your gateway.
Watched for drift
If Ensembl MCP Server adds or changes tools later, gate re-scans and alerts you — before your AI acts on the change.
Connected in three steps
Connect your gate
Add one gateway URL to Claude, ChatGPT, or any MCP client. One-time setup, about two minutes.
Pick Ensembl MCP Server
Choose Ensembl MCP Server in the gate directory. No sign-in needed.
Use it anywhere
Ensembl MCP Server's tools are live in every AI client you've connected — with rules and logging built in.
Free to start · No credit card · No hosting needed
The actual tools Ensembl MCP Server exposes
Fetched live from the official endpoint and re-checked daily by gate — not marketing copy.
ensembl_list_species — List species supported by Ensembl with display name, common name, assembly, taxon ID, and division. Required discovery step — species names
ensembl_lookup_gene — Resolve a gene by symbol + species (or by stable ID) to its Ensembl ID, genomic location (chr:start-end:strand), biotype, description, and t
ensembl_get_sequence — Fetch the DNA, cDNA, CDS, or protein sequence for a gene, transcript, protein, or genomic region. Returns the sequence with its stable ID, m
ensembl_query_region — Find genomic features overlapping a chromosomal region: genes, transcripts, variants, regulatory elements, or exons. Returns each feature wi
ensembl_predict_variant — Predict the functional consequences of a sequence variant using the Ensembl Variant Effect Predictor (VEP). Accepts three input formats: HGV
ensembl_get_homology — Find orthologs and/or paralogs of a gene across species. Returns each homolog's stable ID, species, homology type (ortholog_one2one, ortholo
ensembl_get_xrefs — Retrieve cross-database references for a gene or feature — HGNC, UniProt, EntrezGene, OMIM, RefSeq, Reactome, and others. Returns each xref
Who runs the Ensembl MCP Server MCP server?
The Ensembl MCP Server MCP server at a glance
https://ensembl.caseyjhand.com/mcpQuestions, answered
Is there an official Ensembl MCP Server MCP server?
Yes — Ensembl MCP Server operates its own remote MCP server at ensembl.caseyjhand.com. gate connects you to that official endpoint and adds security scanning, per-tool access rules, and an activity log on top.
How do I connect Ensembl MCP Server to Claude or ChatGPT?
Add gate's gateway URL to your AI client once, then pick Ensembl MCP Server in the directory. No account or sign-in is needed. From then on, Ensembl MCP Server's tools are available in every client you've connected to gate.
Do I need to host anything?
No. Ensembl MCP Server runs the server, and gate is fully managed. You just connect one URL — there's nothing to install, deploy, or maintain.
Is the Ensembl MCP Server MCP server safe to connect?
It's the vendor's official endpoint, and gate scans its tools for prompt injection and hidden instructions before it goes live, re-checks it whenever it changes, and lets you allow, block, or require approval for every single tool.
Is it free?
Yes — you can get started with gate for free and connect Ensembl MCP Server in minutes. No credit card required.
Connect more than just Ensembl MCP Server
Every server below works through the same gateway URL — connect once, add tools anytime.
Squarespace DomainsDesignView →Set up Ensembl MCP Server in: Claude · Claude Code · ChatGPT · Cursor · VS Code
Give your AI Ensembl MCP Server — safely.
One URL. All MCPs. Full control. Free to start.
Get started free