MCP server

Ensembl

io.github.pipeworx-io/ensembl

Checked 26 Oct 2026, 08:29 UTC · Connected to it and listed its tools

Ensembl REST MCP.

Website Source

At a glance

Type

MCP server

Publisher

pipeworx.io (verified by the MCP Registry)

Status

Working at last check

Tools

49

Token cost

About 28,080 tokens per request

Sets up in

Claude Code, Claude Desktop, Codex, Gemini CLI, Cursor, VS Code, Antigravity, ChatGPT, OpenAI API, Grok

Last checked

26 Oct 2026, 08:29 UTC

Connect it to your agent

Add to CursorAdd to VS CodeVS Code Insiders

Opens the app, which shows the server and asks you to confirm. For other apps, copy the setup below.

Claude Code

claude mcp add --transport http ensembl https://gateway.pipeworx.io/ensembl/mcp

Claude Desktop

Settings → Connectors → Add custom connector, and paste the URL.

Codex (config.toml)

[mcp_servers.ensembl]
url = "https://gateway.pipeworx.io/ensembl/mcp"

Gemini CLI

{"mcpServers":{"ensembl":{"httpUrl":"https://gateway.pipeworx.io/ensembl/mcp"}}}

Cursor

{"mcpServers":{"ensembl":{"url":"https://gateway.pipeworx.io/ensembl/mcp"}}}

VS Code

{"servers":{"ensembl":{"type":"http","url":"https://gateway.pipeworx.io/ensembl/mcp"}}}

Antigravity

agy mcp add ensembl https://gateway.pipeworx.io/ensembl/mcp

ChatGPT

Settings → Apps & Connectors → Advanced settings: turn on Developer mode, then Create a connector and paste the URL. Which plans can do this varies.

OpenAI API (Responses tools)

{"type":"mcp","server_label":"ensembl","server_url":"https://gateway.pipeworx.io/ensembl/mcp","require_approval":"always"}

Grok (xAI API tools)

{"type":"mcp","server_label":"ensembl","server_url":"https://gateway.pipeworx.io/ensembl/mcp"}

Tools

• homology ~185 tokens
  "What's the mouse / rat / zebrafish ortholog of [human gene]" / "ortholog of [gene] in [species]" / "homologs of [gene]" — orthologs and paralogs for a gene across species. Use for cross-species comparison, model organism work, evolutionary analysis.
• lookup ~273 tokens
  "Ensembl gene info for [ENSG...]" / "look up [Ensembl ID]" / "fetch [ENST.../ENSE.../ENSP...]" — fetch metadata for an Ensembl stable ID (gene / transcript / exon / translation). Returns name, biotype, chromosomal position, strand, description. Pass expand=true to include child features (transcripts
• lookup_symbol ~287 tokens
  "What's the Ensembl ID for [gene symbol]" / "look up [gene] in Ensembl" / "BRCA1 / TP53 / BRAF Ensembl info" / "find gene [symbol] in [species]" — look up a gene by symbol within a species (e.g. species="human" symbol="BRCA1"). Returns Ensembl gene ID, chromosomal position, biotype, description. Use
• sequence ~251 tokens
  "DNA / cDNA / CDS / protein sequence of [gene]" / "FASTA for [Ensembl ID]" / "get sequence of [transcript]" — sequence by Ensembl stable ID. Type defaults to "genomic"; pass "cdna", "cds", or "protein" for processed forms. Use for sequence retrieval in primer design, variant analysis, or downstream
• variation ~229 tokens
  "What is [rsID]" / "look up SNP [rs...]" / "variant info for [rsN]" — fetch a genetic variation record by ID (e.g. rs56116432). Returns alleles, genomic location, clinical significance, gene mappings. Use for SNP lookups, pharmacogenomics, GWAS follow-up.
• vep ~424 tokens
  "What's the effect of [variant]" / "predict consequences of [genomic change]" / "VEP for [chrom:pos]" — Variant Effect Predictor for a specified region + allele. Returns consequences (missense, synonymous, splice, etc.), affected genes, transcript impacts, SIFT/PolyPhen predictions. Use for variant
• xrefs ~128 tokens
  "What's the UniProt / HGNC / RefSeq ID for [gene]" / "cross-references for [gene symbol]" — external database IDs (UniProt, RefSeq, HGNC, Entrez, OMIM, etc.) for a gene symbol. Use to map between bio-database identifier spaces.

Browse

• GitHub tools
• GitHub and code hosting
• Databases
• Translation

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