ensembl_get_sequence
ActiveTool of io.github.cyanheads/ensembl-mcp-server
Fetch the DNA, cDNA, CDS, or protein sequence for a gene, transcript, protein, or genomic region. Returns the sequence with its stable ID, molecule type, and character count — large sequences are returned in full but the length is stated so callers can budget context. 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 the format species:chr:start-end (e.g. homo_sapiens:13:32315086-32400268) and set species. 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.
Parameters schema
{
"type": "object",
"$schema": "http://json-schema.org/draft-07/schema#",
"required": [
"id"
],
"properties": {
"id": {
"type": "string",
"description": "Ensembl stable ID (ENSG…, ENST…, ENSP…) or region in the format species:chr:start-end (e.g. homo_sapiens:13:32315086-32400268) for region mode. For genomic region queries, species is also required."
},
"type": {
"enum": [
"genomic",
"cdna",
"cds",
"protein"
],
"type": "string",
"default": "genomic",
"description": "Sequence type to retrieve. genomic: full genomic DNA including introns (default). cdna: spliced transcript sequence (requires ENST… ID). cds: coding sequence only, no UTRs (requires ENST… ID with coding transcript). protein: amino acid sequence (requires ENST… or ENSP… ID)."
},
"species": {
"type": "string",
"description": "Species in Ensembl internal format (e.g. homo_sapiens). Required for region mode (when id is a species:chr:start-end string). Optional for stable ID lookups — Ensembl infers species from the ID prefix."
},
"expand_3prime": {
"type": "integer",
"default": 0,
"maximum": 9007199254740991,
"minimum": 0,
"description": "Number of base pairs to extend downstream (3' direction) of the requested feature. Default 0. Only applies to genomic sequences and region queries."
},
"expand_5prime": {
"type": "integer",
"default": 0,
"maximum": 9007199254740991,
"minimum": 0,
"description": "Number of base pairs to extend upstream (5' direction) of the requested feature. Default 0. Only applies to genomic sequences and region queries."
}
}
}Parent server
io.github.cyanheads/ensembl-mcp-server
https://github.com/cyanheads/ensembl-mcp-server
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