ensembl_mapping
Convert genomic coordinates between different systems (e.g., cDNA, CDS, protein, assemblies) using specified feature IDs and mapping types. Supports multiple species and assembly conversions for precise genomic data analysis.
Instructions
Map coordinates between different coordinate systems (genomic ↔ cDNA/CDS/protein) and between genome assemblies. Covers /map/* endpoints.
Input Schema
| Name | Required | Description | Default |
|---|---|---|---|
| coordinates | Yes | Coordinates to map: '100..200' for cDNA/CDS coords, or 'chr:start-end' for genomic (e.g., '100..300', '1..150', '17:7565096-7590856', 'X:1000000-2000000') | |
| feature_id | No | Feature ID (transcript/translation) for coordinate mapping (e.g., 'ENST00000288602', 'ENSP00000288602') | |
| mapping_type | Yes | Type of coordinate mapping | |
| source_assembly | No | Source assembly name (for assembly mapping) (e.g., 'GRCh37', 'GRCh38') | |
| species | No | Species name (e.g., 'homo_sapiens', 'mus_musculus') | homo_sapiens |
| target_assembly | No | Target assembly name (for assembly mapping) (e.g., 'GRCh38', 'GRCh37') |