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Ensembl MCP Server

ensembl_sequence

Retrieve DNA, RNA, or protein sequences for genes, transcripts, or genomic regions. Specify species, sequence type, and output format to extract precise genomic data from the Ensembl database.

Instructions

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

Input Schema

NameRequiredDescriptionDefault
formatNoOutput formatjson
identifierYesFeature ID (gene, transcript, etc.) OR genomic region in format 'chr:start-end' (e.g., 'ENSG00000141510', 'ENST00000288602', '17:7565096-7590856', 'X:1000000-2000000')
maskNoMask repeats (soft=lowercase, hard=N)
sequence_typeNoType of sequence to retrievegenomic
speciesNoSpecies 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" }

MCP directory API

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curl -X GET 'https://glama.ai/api/mcp/v1/servers/effieklimi/ensembl-mcp-server'

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