ensembl-mcp-server

Quality 85 / 100good

7 tools, about 5,517 tokens to load them all · tool set 8fcfdbccee5b · tools last changed 2026-10-19 · checked 2026-10-19 20:06 UTC

Tool changes

• 2026-10-19ensembl_get_xrefschangeddescription, input schema, output schema
  before

  Retrieve cross-database references for a gene or feature — HGNC, UniProt, EntrezGene, OMIM, RefSeq, Reactome, and others. Returns each xref with its database name, primary ID, display ID, and description. The dbname filter narrows to specific databases; omit to return all xrefs. IDs returned here chain to protein (pubchem via UniProt), literature (pubmed via PubMed IDs), disease (OMIM via MIM_GENE), and pathway (Reactome) resources. Requires an Ensembl stable ID — use ensembl_lookup_gene to get the ENSG… ID first. Common dbname values: HGNC, Uniprot_gn, EntrezGene, MIM_GENE, RefSeq_mRNA, RefSeq_peptide, Reactome, GO (Gene Ontology), ChEMBL.

  after · 75% of words in common

  Retrieve cross-database references for a gene or feature — HGNC, UniProt, EntrezGene, OMIM, RefSeq, Reactome, and others. Returns each xref with its database name, primary ID, display ID, and description. By default only the requested object level is queried; all_levels=true includes transcript and translation references for a gene. The dbname filter narrows this scope. IDs returned here chain to protein (pubchem via UniProt), literature (pubmed via PubMed IDs), disease (OMIM via MIM_GENE), and pathway (Reactome) resources. Requires an Ensembl stable ID — use ensembl_lookup_gene to get the ENSG… ID first. Common dbname values: HGNC, Uniprot_gn, EntrezGene, MIM_GENE, RefSeq_mRNA, RefSeq_peptide, Reactome_gene (gene pathways), Reactome (translation pathways), GO (Gene Ontology), ChEMBL.

• 2026-10-19ensembl_get_homologychangeddescription, output schema
  before

  Find orthologs and/or paralogs of a gene across species. Returns each homolog's stable ID, species, homology type (ortholog_one2one, ortholog_one2many, paralog_many2many, etc.), perc_id (percent identity), perc_pos (percent positives), and taxonomy level. Essential for cross-species research — for example, "what is the mouse equivalent of human TP53?" or "how conserved is BRCA2 across mammals?". Provide either symbol + species or a stable gene ID. Target species can be filtered to a single species or left open to return all available homologs.

  after · 67% of words in common

  Find orthologs and/or paralogs of a gene across species. Returns each homolog's stable ID, species, homology type (ortholog_one2one, ortholog_one2many, paralog_many2many, etc.), percId (percent identity), percPos (percent positives), and taxonomy level. Essential for cross-species research — for example, "what is the mouse equivalent of human TP53?" or "how conserved is BRCA2 across mammals?". Provide either symbol + species or a stable gene ID. Target species can be filtered to a single species or left open to return all available homologs. Includes targetProteinId when available for ensembl_get_sequence with type="protein". targetSymbol is best-effort: a secondary gene lookup shares five seconds across the returned rows and the remaining call deadline; missing names never remove homologs.

• 2026-10-19ensembl_predict_variantchangedoutput schema
• 2026-10-19ensembl_query_regionchangedinput schema
• 2026-10-19ensembl_get_sequencechangeddescription
  before

  Fetch the DNA, cDNA, CDS, or protein sequence for a gene, transcript, protein, or genomic region. Returns a window of the sequence — the first 10,000 characters by default — with its stable ID, molecule type, and full length. When more follows the window, truncated is true and nextOffset is the offset to request next; walking nextOffset reconstructs the whole sequence, and max_length 0 returns everything from offset to the end. The type parameter selects which sequence is fetched: genomic (default, includes introns), cdna (spliced transcript), cds (coding sequence only), protein. For region mode, set id to a region — either species:chr:start-end (e.g. homo_sapiens:13:32315086-32400268) or a bare chr:start-end with species set (e.g. id 13:32315086-32400268, species homo_sapiens), spanning at most 10,000,000 bases; a :-1 suffix (13:32315086-32315100:-1) returns the reverse-strand sequence. Regions return genomic DNA only. Protein sequences require a transcript or protein stable ID (ENST…/ENSP…), not a gene ID — use ensembl_lookup_gene with expand_transcripts=true to get the canonical transcript ID first.

  after · 91% of words in common

  Fetch the DNA, cDNA, CDS, or protein sequence for a gene, transcript, protein, or genomic region. Returns a window of the sequence — the first 10,000 characters by default — with its stable ID, molecule type, and full length. When more follows the window, truncated is true and nextOffset is the offset to request next; walking nextOffset reconstructs the whole sequence, and max_length 0 returns everything from offset to the end. The type parameter selects which sequence is fetched: genomic (default, includes introns), cdna (spliced transcript), cds (coding sequence only), protein. For region mode, set id to a region — either species:chr:start-end (e.g. homo_sapiens:13:32315086-32400268) or a bare chr:start-end with species set (e.g. id 13:32315086-32400268, species homo_sapiens), spanning at most 10,000,000 bases; a :-1 suffix (13:32315086-32315100:-1) returns the reverse-strand sequence. Regions return genomic DNA only. Protein sequences require a transcript or protein stable ID (ENST…/ENSP…), not a gene ID — use ensembl_lookup_gene and its canonicalTranscript field first; expand_transcripts=true also supplies transcript biotypes and MANE Select accessions.

• 2026-10-19ensembl_lookup_genechangeddescription, input schema, output schema
  before

  Resolve a gene by symbol + species (or by stable ID) to its Ensembl ID, genomic location (chr:start-end:strand), biotype, description, and transcript list. Entry point for most workflows — the stable ID and coordinates returned here are inputs to other tools. Accepts both symbol lookup (BRCA2 + homo_sapiens) and direct ID lookup (ENSG00000139618). A symbol that is not a current gene name is matched against synonyms and former symbols (HER2 → ERBB2), reported as matchedAlias; when it maps to several genes the result is ambiguous, listing the candidates to retry by id. Supports batch lookup of up to 20 IDs or symbols in one call via the ids or symbols field. Provide exactly one of symbol, id, ids, or symbols. For symbol lookups species defaults to homo_sapiens (override for other organisms); for ID lookups species is not needed. Use ensembl_list_species with nameContains (a genus or common name) to find valid species names.

  after · 86% of words in common

  Resolve a gene by symbol + species (or by stable ID) to its Ensembl ID, genomic location (chr:start-end:strand), biotype, description, and transcript list. Entry point for most workflows — the stable ID and coordinates returned here are inputs to other tools. Accepts both symbol lookup (BRCA2 + homo_sapiens) and direct ID lookup (ENSG00000139618). A symbol that is not a current gene name is matched against synonyms and former symbols (HER2 → ERBB2), reported as matchedAlias; when it maps to several genes the result is ambiguous, listing the candidates to retry by id. Supports batch submission of up to 1,000 IDs or symbols: the first 20 distinct queries are resolved, and batch.omitted names the unattempted remainder to resubmit. Provide exactly one of symbol, id, ids, or symbols. For symbol lookups species defaults to homo_sapiens (override for other organisms); for ID lookups species is not needed. Use ensembl_list_species with nameContains (a genus or common name) to find valid species names.

• 2026-10-14ensembl_get_xrefschangedinput schema, output schema
• 2026-10-14ensembl_get_homologychangedinput schema, output schema
• 2026-10-14ensembl_predict_variantchangedinput schema, output schema
• 2026-10-14ensembl_query_regionchangeddescription, input schema, output schema
  before

  Find genomic features overlapping a chromosomal region: genes, transcripts, variants, regulatory elements, or exons. Returns each feature with its stable ID, type, location, biotype, and name, plus the genome assembly the coordinates are on. Useful for "what's in this locus?" and for seeding follow-up lookups. Region format is chr:start-end (e.g. 13:32315086-32400268 for the BRCA2 locus), spanning at most 5,000,000 bases. Ensembl normalizes chromosome names and canonical vertebrate output omits the chr prefix (13, not chr13); a chr-prefixed name like chr13 is also accepted. The feature parameter defaults to gene only — requesting variation in an 85 kb region matches 44,000+ entries. Explicitly include variation, regulatory, transcript, or exon only when needed. The response returns up to max_results features (default 100) while totalCount always reports the full count; set max_results to 0 for every feature, or query a smaller region to see a different slice. Exon rows carry the parent transcript ID, so the same exon appears once per transcript it belongs to.

  after · 98% of words in common

  Find genomic features overlapping a chromosomal region: genes, transcripts, variants, regulatory elements, or exons. Returns each feature with its stable ID, type, location, biotype, and name, plus the genome assembly the coordinates are on. Useful for "what's in this locus?" and for seeding follow-up lookups. Region format is chr:start-end with species set (e.g. 13:32315086-32400268 for the BRCA2 locus), or species:chr:start-end (e.g. homo_sapiens:13:32315086-32400268), spanning at most 5,000,000 bases. Ensembl normalizes chromosome names and canonical vertebrate output omits the chr prefix (13, not chr13); a chr-prefixed name like chr13 is also accepted. The feature parameter defaults to gene only — requesting variation in an 85 kb region matches 44,000+ entries. Explicitly include variation, regulatory, transcript, or exon only when needed. The response returns up to max_results features (default 100) while totalCount always reports the full count; set max_results to 0 for every feature, or query a smaller region to see a different slice. Exon rows carry the parent transcript ID, so the same exon appears once per transcript it belongs to.

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