Ensembl MCP Server
Server Configuration
Describes the environment variables required to run the server.
| Name | Required | Description | Default |
|---|---|---|---|
No arguments | |||
Instructions
Guidance the server publishes about itself, which clients place ahead of the tool catalog so the model reads it before choosing anything.
This server publishes no instructions, or was last inspected before Glama recorded them.
Capabilities
Server capabilities have not been inspected yet.
Tools
Functions exposed to the LLM to take actions
| Name | Description |
|---|---|
| lookup_geneC | Get detailed gene information by stable ID or symbol |
| get_transcriptsC | Get all transcripts for a gene with detailed structure |
| search_genesC | Search for genes by name, description, or identifier |
| get_sequenceC | Get DNA sequence for genomic coordinates or gene/transcript ID |
| get_cds_sequenceB | Get coding sequence (CDS) for a transcript |
| translate_sequenceC | Translate DNA sequence to protein sequence |
| get_homologsC | Find orthologous and paralogous genes across species |
| get_gene_treeC | Get phylogenetic tree for gene family |
| get_variantsC | Get genetic variants in a genomic region |
| get_variant_consequencesC | Predict consequences of variants on genes and transcripts |
| get_regulatory_featuresC | Get regulatory elements (enhancers, promoters, TFBS) in genomic region |
| get_motif_featuresC | Get transcription factor binding motifs in genomic region |
| get_xrefsC | Get external database cross-references for genes |
| map_coordinatesB | Convert coordinates between genome assemblies |
| list_speciesC | Get list of available species and assemblies |
| get_assembly_infoC | Get genome assembly information and statistics |
| get_karyotypeC | Get chromosome information and karyotype |
| batch_gene_lookupC | Look up multiple genes simultaneously |
| batch_sequence_fetchC | Fetch sequences for multiple regions or features |
Prompts
Interactive templates invoked by user choice
| Name | Description |
|---|---|
No prompts | |
Resources
Contextual data attached and managed by the client
| Name | Description |
|---|---|
No resources | |
TDQS
Scored across 19 tools
Every tool has a clearly distinct purpose with no ambiguity. For example, 'lookup_gene' retrieves detailed gene information, 'search_genes' finds genes by name or description, and 'get_transcripts' focuses on transcript structures, ensuring agents can easily differentiate between them.
All tool names follow a consistent verb_noun pattern using snake_case, such as 'get_sequence', 'list_species', and 'search_genes'. This uniformity makes the toolset predictable and easy to navigate for agents.
With 19 tools, the server is well-scoped for genomic data analysis, covering diverse operations like sequence fetching, variant analysis, and gene lookups. Each tool earns its place without feeling excessive or insufficient for the domain.
The toolset provides complete coverage for genomic workflows, including data retrieval (e.g., 'get_sequence'), analysis (e.g., 'get_variant_consequences'), and utilities (e.g., 'map_coordinates'). There are no obvious gaps, supporting comprehensive agent operations in this domain.