ensembl_sequence

Retrieve DNA, RNA, or protein sequences by specifying a gene, transcript, or genomic region. Supports genomic, cDNA, CDS, and protein sequence types with output in JSON or FASTA format.

Instructions

Retrieve DNA, RNA, or protein sequences for genes, transcripts, regions. Covers /sequence/id and /sequence/region endpoints.

Input Schema

Name	Required	Description	Default
`format`	No	Output format	json
`identifier`	Yes	Feature ID (gene, transcript, etc.) OR genomic region in format 'chr:start-end' (e.g., 'ENSG00000141510', 'ENST00000288602', '17:7565096-7590856', 'X:1000000-2000000')
`mask`	No	Mask repeats (soft=lowercase, hard=N)
`sequence_type`	No	Type of sequence to retrieve	genomic
`species`	No	Species name (e.g., 'homo_sapiens', 'mus_musculus')	homo_sapiens

Input Schema (JSON Schema)

{
  "properties": {
    "format": {
      "default": "json",
      "description": "Output format",
      "enum": [
        "json",
        "fasta"
      ],
      "type": "string"
    },
    "identifier": {
      "description": "Feature ID (gene, transcript, etc.) OR genomic region in format 'chr:start-end' (e.g., 'ENSG00000141510', 'ENST00000288602', '17:7565096-7590856', 'X:1000000-2000000')",
      "type": "string"
    },
    "mask": {
      "description": "Mask repeats (soft=lowercase, hard=N)",
      "enum": [
        "soft",
        "hard"
      ],
      "type": "string"
    },
    "sequence_type": {
      "default": "genomic",
      "description": "Type of sequence to retrieve",
      "enum": [
        "genomic",
        "cdna",
        "cds",
        "protein"
      ],
      "type": "string"
    },
    "species": {
      "default": "homo_sapiens",
      "description": "Species name (e.g., 'homo_sapiens', 'mus_musculus')",
      "type": "string"
    }
  },
  "required": [
    "identifier"
  ],
  "type": "object"
}

Ensembl MCP Server

ensembl_sequence

Instructions

Input Schema

Input Schema (JSON Schema)

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