Server Configuration
Describes the environment variables required to run the server.
| Name | Required | Description | Default |
|---|---|---|---|
| REQUEST_TIMEOUT | No | Set custom timeout (default: 30000ms) | |
| ENSEMBL_BASE_URL | No | Override default API base URL |
Schema
Prompts
Interactive templates invoked by user choice
| Name | Description |
|---|---|
No prompts | |
Resources
Contextual data attached and managed by the client
| Name | Description |
|---|---|
No resources | |
Tools
Functions exposed to the LLM to take actions
| Name | Description |
|---|---|
| lookup_gene | Get detailed gene information by stable ID or symbol |
| get_transcripts | Get all transcripts for a gene with detailed structure |
| search_genes | Search for genes by name, description, or identifier |
| get_sequence | Get DNA sequence for genomic coordinates or gene/transcript ID |
| get_cds_sequence | Get coding sequence (CDS) for a transcript |
| translate_sequence | Translate DNA sequence to protein sequence |
| get_homologs | Find orthologous and paralogous genes across species |
| get_gene_tree | Get phylogenetic tree for gene family |
| get_variants | Get genetic variants in a genomic region |
| get_variant_consequences | Predict consequences of variants on genes and transcripts |
| get_regulatory_features | Get regulatory elements (enhancers, promoters, TFBS) in genomic region |
| get_motif_features | Get transcription factor binding motifs in genomic region |
| get_xrefs | Get external database cross-references for genes |
| map_coordinates | Convert coordinates between genome assemblies |
| list_species | Get list of available species and assemblies |
| get_assembly_info | Get genome assembly information and statistics |
| get_karyotype | Get chromosome information and karyotype |
| batch_gene_lookup | Look up multiple genes simultaneously |
| batch_sequence_fetch | Fetch sequences for multiple regions or features |