get_sequence

Retrieve DNA sequences for specified genomic coordinates, gene IDs, or transcript IDs. Supports multiple species, output formats (JSON or FASTA), and optional repeat masking. Part of the Ensembl MCP Server for genomic data access.

Instructions

Get DNA sequence for genomic coordinates or gene/transcript ID

Input Schema

Name	Required	Description
`format`	No	Output format (default: fasta)
`mask`	No	Repeat masking type (optional)
`multiple_sequences`	No	Return multiple sequences if applicable (default: false)
`region`	Yes	Genomic region (chr:start-end) or feature ID
`species`	No	Species name (default: homo_sapiens)

Input Schema (JSON Schema)

{
  "properties": {
    "format": {
      "description": "Output format (default: fasta)",
      "enum": [
        "json",
        "fasta"
      ],
      "type": "string"
    },
    "mask": {
      "description": "Repeat masking type (optional)",
      "enum": [
        "hard",
        "soft"
      ],
      "type": "string"
    },
    "multiple_sequences": {
      "description": "Return multiple sequences if applicable (default: false)",
      "type": "boolean"
    },
    "region": {
      "description": "Genomic region (chr:start-end) or feature ID",
      "type": "string"
    },
    "species": {
      "description": "Species name (default: homo_sapiens)",
      "type": "string"
    }
  },
  "required": [
    "region"
  ],
  "type": "object"
}

Ensembl MCP Server

get_sequence

Instructions

Input Schema

Input Schema (JSON Schema)

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MCP directory API