Ensembl MCP Server

MIT License

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get_sequence

Retrieve DNA sequences for specified genomic regions or gene/transcript IDs. Supports multiple species, repeat masking, and output formats like FASTA or JSON using the Ensembl MCP Server.

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"
}

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