@pipeworx/ensembl

Connect: https://gateway.pipeworx.io/ensembl/mcp · Install: one-click buttons

Tools: 7

Ensembl REST API MCP — vertebrate genomes, gene annotations, sequences, comparative genomics, variation. Keyless.

Tools

• lookup(id, expand?) — by stable id (gene/transcript/exon/translation)
• lookup_symbol(species, symbol) — gene by symbol within a species
• xrefs(species, symbol) — external cross-references for a gene symbol
• sequence(id, type?) — DNA / cDNA / CDS / protein sequence
• homology(species, symbol_or_id, target_species?) — homology mappings
• variation(species, variant_id) — variation by name (e.g. “rs56116432”)
• vep(species, region, allele) — Variant Effect Predictor (region: “9:22125504-22125504:1”)
• xref_symbol(species, symbol) — symbol lookup (alias for /xrefs/symbol)

Data source

https://rest.ensembl.org

Tools

• lookup — “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
• lookup_symbol — “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. speci
• xrefs — “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-
• sequence — “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
• homology — “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 compa
• variation — “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.
• vep — “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, synony