effieklimi/ensembl-mcp-server
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The Ensembl API MCP Server is a comprehensive Model Context Protocol server that provides access to Ensembl's REST API, designed for biologists and developers.
Tools
Functions exposed to the LLM to take actions
ensembl_feature_overlap
Find genes, transcripts, or regulatory elements that overlap a region or another feature.
ensembl_regulatory
Regulatory features, binding matrices and related annotations.
ensembl_protein_features
Protein-level domains and functional sites.
ensembl_meta
Server metadata, species lists, release info, and diagnostics.
ensembl_lookup
Translate IDs ↔ symbols, pull xrefs, recode variants.
ensembl_sequence
Retrieve DNA, RNA or protein sequences.
ensembl_mapping
Coordinate conversion (genome ↔ cDNA/CDS/protein) and assembly lift-over.
ensembl_compara
Comparative genomics—homology, gene trees, alignments.
ensembl_variation
Variant lookup, VEP consequences, LD, phenotype mapping.
ensembl_ontotax
Ontology term search and NCBI taxonomy traversal.
Prompts
Interactive templates invoked by user choice
No prompts
Resources
Contextual data attached and managed by the client