Ensembl MCP Server

Find genomic features (genes, transcripts, regulatory elements) that overlap with a genomic region or specific feature. Automatically handles assembly-specific format variations (GRCh38/hg38, chromosome naming conventions, coordinate systems). Covers /overlap/region and /overlap/id endpoints.

Get regulatory features, binding matrices, and regulatory annotations. Covers regulatory overlap endpoints and binding matrix data.

Get protein-level features, domains, and annotations for proteins and translations.

Get server metadata, data releases, species info, and system status. Covers /info/* endpoints and /archive/id for version tracking.

Look up genes, transcripts, variants by ID or symbol. Get cross-references and perform ID translation. Covers /lookup/* and /xrefs/* endpoints plus variant_recoder.

Retrieve DNA, RNA, or protein sequences for genes, transcripts, regions. Covers /sequence/id and /sequence/region endpoints.

Map coordinates between different coordinate systems (genomic ↔ cDNA/CDS/protein) and between genome assemblies. Covers /map/* endpoints.

Comparative genomics: gene trees, homology, species alignments, and evolutionary analysis. Covers /genetree/, /homology/, /alignment/* endpoints.

Variant analysis: VEP consequence prediction, variant lookup, LD analysis, phenotype mapping, haplotypes. Covers /variation/, /vep/, /ld/, /phenotype/ endpoints.

Ontology term search and NCBI taxonomy traversal. Search GO terms, phenotype ontologies, and taxonomic classifications.