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Ensembl

Ensembl MCP Connector for Claude

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Access genomic data, gene trees, homologies, and cross-references from the Ensembl database directly from any AI agent.

27 tools Official Updated Oct 1, 2026 Official Vinkius Partner
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Connect to the Ensembl REST API to perform advanced genomic research and biological data retrieval through natural conversation.

What you can do

  • Comparative Genomics — Retrieve gene trees, homologies (orthologs/paralogs), and genomic alignments across multiple species.
  • Archive & Lookup — Fetch the latest versions of stable identifiers and look up current metadata for genes and transcripts.
  • Cross References (Xrefs) — Link Ensembl objects to external databases using symbols (e.g., BRCA2) or specific external IDs.
  • Species Metadata — List all available species in the Ensembl database and retrieve their specific assembly information.
  • Sequence Analysis — Access genomic sequences by ID or region, and perform variant effect prediction (VEP) queries.

How it works

  1. Subscribe to this server
  2. Enter your API configuration (use 'PUBLIC' for standard access)
  3. Start querying genomic data from Claude, Cursor, or any MCP-compatible client

Who is this for?

  • Bioinformaticians — quickly pull gene trees and homology data without writing custom Python or R scripts
  • Genomic Researchers — verify stable ID versions and cross-reference symbols directly from their research environment
  • Data Scientists — automate the retrieval of genomic alignments and metadata for large-scale biological analysis
genomicsbioinformaticsgene-treesdna-sequencingbiological-data

27 tools expose this connector's capabilities to your AI agent.

get_xrefs_symbol

Look up an external symbol and return linked Ensembl objects

get_archive_bulk

Retrieve the latest version for a set of identifiers

get_archive_id

Returns the latest version of a given identifier

get_ga4gh_beacon

Beacon service for allele information

get_homology

Retrieves homology information by species and gene ID

get_ld

Compute Linkage Disequilibrium (LD) values

get_lookup_bulk

Bulk lookup for multiple identifiers

search_ga4gh_variants

Search for variants using GA4GH schema

get_lookup_id

Find the species and database for a single identifier

get_map_cdna

Convert cDNA coordinates to genomic coordinates

get_ontology_id

Search for an ontological term by its identifier

get_overlap_region

) overlapping a region. Retrieve features overlapping a specific region

ping

Check if the service is alive

get_taxonomy_id

Search for a taxonomic term by ID or name

get_variation

Retrieve variant features, genotypes, and population data

get_vep_bulk

Bulk consequence prediction for multiple regions

get_vep_hgvs

Fetch consequences for a variant in HGVS notation

get_alignment

Retrieves genomic alignments for a specific region

get_genetree

Retrieves a gene tree for a stable identifier

get_info_assembly

List available assemblies and chromosomes for a species

get_info_rest

Current version of the Ensembl REST API

get_info_species

Lists all available species and their metadata

get_map

Convert coordinates from one assembly version to another

get_sequence_id

Request sequence by stable identifier

get_sequence_region

Request genomic sequence by region

get_vep_id

Fetch consequences for a variant identifier (e.g., rsID)

get_xrefs_id

Retrieve external references for an Ensembl identifier

See how to talk to your AI agent using Ensembl.

What is the latest version of the Ensembl identifier ENSG00000139618?

I've checked the archive for ENSG00000139618. The latest version is version 11, which is currently active in the latest assembly.

Find all orthologues for the human gene ENSG00000139618 in mouse.

Searching homologies... I found 1 high-confidence orthologue in Mus musculus: ENSMUSG00000041147 (Brca2). Would you like the alignment details?

List all species currently available in the Ensembl database.

I've retrieved the species list. There are over 300 species available, including Homo sapiens, Mus musculus, Danio rerio, and many others. Do you want to filter by a specific taxon?

Use the `get_homology` tool by providing the species name and the Ensembl gene ID. You can filter by type (e.g., 'orthologues') to see related genes in other organisms.

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