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 |