ensembl_compara

Analyze gene trees, identify homology, explore species alignments, and perform evolutionary analysis using comparative genomics. Supports gene IDs, symbols, regions, and species-specific queries.

Instructions

Comparative genomics: gene trees, homology, species alignments, and evolutionary analysis. Covers /genetree/, /homology/, /alignment/* endpoints.

Input Schema

Name	Required	Description	Default
`aligned`	No	Include aligned sequences
`analysis_type`	No	Type of comparative analysis
`gene_id`	No	Gene ID for homology/gene tree analysis (e.g., 'ENSG00000141510', 'ENSG00000012048')
`gene_symbol`	No	Gene symbol (alternative to gene_id) (e.g., 'BRCA1', 'TP53', 'EGFR')
`homology_type`	No	Type of homology to retrieve	all
`region`	No	Genomic region for alignments in format 'chr:start-end' (e.g., '17:7565096-7590856', 'X:1000000-2000000', '6:25000000-35000000')
`species`	No	Species name (e.g., 'homo_sapiens', 'mus_musculus', 'pan_troglodytes')	homo_sapiens
`target_species`	No	Target species for homology search (e.g., 'mus_musculus', 'pan_troglodytes', 'rattus_norvegicus')

Input Schema (JSON Schema)

{
  "anyOf": [
    {
      "required": [
        "gene_id",
        "analysis_type"
      ]
    },
    {
      "required": [
        "gene_symbol",
        "analysis_type"
      ]
    },
    {
      "required": [
        "region",
        "analysis_type"
      ]
    }
  ],
  "properties": {
    "aligned": {
      "default": false,
      "description": "Include aligned sequences",
      "type": "boolean"
    },
    "analysis_type": {
      "description": "Type of comparative analysis",
      "enum": [
        "homology",
        "genetree",
        "cafe_tree",
        "alignment"
      ],
      "type": "string"
    },
    "gene_id": {
      "description": "Gene ID for homology/gene tree analysis (e.g., 'ENSG00000141510', 'ENSG00000012048')",
      "type": "string"
    },
    "gene_symbol": {
      "description": "Gene symbol (alternative to gene_id) (e.g., 'BRCA1', 'TP53', 'EGFR')",
      "type": "string"
    },
    "homology_type": {
      "default": "all",
      "description": "Type of homology to retrieve",
      "enum": [
        "orthologues",
        "paralogues",
        "all"
      ],
      "type": "string"
    },
    "region": {
      "description": "Genomic region for alignments in format 'chr:start-end' (e.g., '17:7565096-7590856', 'X:1000000-2000000', '6:25000000-35000000')",
      "type": "string"
    },
    "species": {
      "default": "homo_sapiens",
      "description": "Species name (e.g., 'homo_sapiens', 'mus_musculus', 'pan_troglodytes')",
      "type": "string"
    },
    "target_species": {
      "description": "Target species for homology search (e.g., 'mus_musculus', 'pan_troglodytes', 'rattus_norvegicus')",
      "type": "string"
    }
  },
  "type": "object"
}

Ensembl MCP Server

ensembl_compara

Instructions

Input Schema

Input Schema (JSON Schema)

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