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"
}