Unofficial Ensembl MCP Server
A comprehensive Model Context Protocol (MCP) server that provides access to the Ensembl REST API for genomic data, comparative genomics, and biological annotations.
Developed by Augmented Nature
Overview
This server enables seamless access to Ensembl's vast genomic database through a standardized MCP interface. It supports gene lookups, sequence retrieval, variant analysis, comparative genomics, regulatory features, and much more across multiple species.
Features
Gene & Transcript Information
- Gene Lookup: Get detailed gene information by Ensembl ID or gene symbol
- Transcript Analysis: Retrieve all transcripts for a gene with structural details
- Gene Search: Search genes by name, description, or identifier with filtering options
Sequence Data
- Genomic Sequences: Extract DNA sequences for any genomic region or feature
- CDS Sequences: Get coding sequences for specific transcripts
- Sequence Translation: Translate DNA sequences to protein sequences
- Repeat Masking: Support for hard and soft repeat masking
Comparative Genomics
- Homolog Detection: Find orthologous and paralogous genes across species
- Phylogenetic Trees: Generate gene family trees in multiple formats
- Cross-Species Analysis: Compare genes and genomes across different organisms
Variant Data
- Variant Retrieval: Get genetic variants in genomic regions
- Consequence Prediction: Predict variant effects on genes and transcripts
- Population Genetics: Access allele frequencies and population data
Regulatory Features
- Regulatory Elements: Access enhancers, promoters, and TFBS data
- Motif Features: Get transcription factor binding motifs
- Cell Type Context: Filter regulatory features by cell type
Cross-References & Annotations
- External Database Links: Get cross-references to PDB, EMBL, RefSeq, etc.
- Coordinate Mapping: Convert coordinates between genome assemblies
- Ontology Terms: Access GO terms and functional annotations
Species & Assembly Information
- Species Lists: Browse available species and assemblies
- Assembly Statistics: Get genome assembly information and statistics
- Karyotype Data: Access chromosome information and banding patterns
Batch Processing
- Batch Gene Lookup: Process multiple genes simultaneously
- Batch Sequence Fetch: Retrieve sequences for multiple regions efficiently
Installation
# Clone or download the server files
cd ensembl-server
# Install dependencies
npm install
# Build the server
npm run build
Usage with Claude Desktop
Setup Instructions
-
Build the server (if not already done):
npm run build -
Add to Claude Desktop configuration:
- Open Claude Desktop
- Go to Settings → MCP Servers
- Add a new server with:
- Name:
ensembl - Command:
node - Args:
/path/to/ensembl-server/build/index.js
- Name:
-
Restart Claude Desktop to load the server
Available Tools (25 total)
Gene & Transcript Information
lookup_gene- Get detailed gene information by stable ID or symbolget_transcripts- Get all transcripts for a gene with detailed structuresearch_genes- Search for genes by name, description, or identifier
Sequence Data
get_sequence- Get DNA sequence for genomic coordinates or gene/transcript IDget_cds_sequence- Get coding sequence (CDS) for a transcripttranslate_sequence- Translate DNA sequence to protein sequence
Comparative Genomics
get_homologs- Find orthologous and paralogous genes across speciesget_gene_tree- Get phylogenetic tree for gene family
Variant Data
get_variants- Get genetic variants in a genomic regionget_variant_consequences- Predict consequences of variants on genes and transcripts
Regulatory Features
get_regulatory_features- Get regulatory elements in genomic regionget_motif_features- Get transcription factor binding motifs in genomic region
Cross-References & Annotations
get_xrefs- Get external database cross-references for genesmap_coordinates- Convert coordinates between genome assemblies
Species & Assembly Information
list_species- Get list of available species and assembliesget_assembly_info- Get genome assembly information and statisticsget_karyotype- Get chromosome information and karyotype
Batch Processing
batch_gene_lookup- Look up multiple genes simultaneouslybatch_sequence_fetch- Fetch sequences for multiple regions or features
Example Usage in Claude Desktop
Once connected, you can use natural language to access genomic data:
- "Look up the BRCA2 gene and get its sequence"
- "Find orthologs of TP53 in mouse"
- "Get variants in the region chr17:43044295-43125364"
- "Search for insulin-related genes"
- "Get the assembly information for human genome"
- "Translate this DNA sequence to protein: ATGAAACGC..."
Supported Species
The server supports all species available in Ensembl, including:
- Vertebrates: Human, Mouse, Rat, Zebrafish, etc.
- Plants: Arabidopsis, Rice, Wheat, etc.
- Fungi: Yeast, etc.
- Protists: Various protist species
- Metazoa: Drosophila, C. elegans, etc.
Default species is homo_sapiens when not specified.
Input Formats
Genomic Regions
chr1:1000000-2000000- Standard format1:1000000-2000000- Without 'chr' prefixENSG00000139618- Feature IDs
Gene/Transcript IDs
- Ensembl IDs:
ENSG00000139618,ENST00000380152 - Gene symbols:
BRCA2,TP53 - RefSeq IDs:
NM_000059
Output Formats
Primary Formats
- JSON: Structured data (default for most tools)
- FASTA: Sequence data
- GFF: Genomic feature format
- VCF: Variant call format
Tree Formats
- JSON: Structured tree data
- Newick: Standard phylogenetic format
- PhyloXML: Rich phylogenetic format
Error Handling
The server provides comprehensive error handling:
- Invalid Parameters: Clear validation messages
- API Errors: Detailed error information from Ensembl
- Network Issues: Timeout and connectivity error handling
- Species Validation: Automatic species name validation
Rate Limiting
The server respects Ensembl's rate limiting guidelines:
- Maximum 15 requests per second
- Appropriate delays between batch operations
- Connection pooling for efficiency
Configuration
Environment Variables
ENSEMBL_BASE_URL: Override default API base URLREQUEST_TIMEOUT: Set custom timeout (default: 30000ms)
Species Configuration
- Default species:
homo_sapiens - Automatic species validation
- Support for all Ensembl divisions
API Coverage
This server provides access to major Ensembl REST API endpoints:
Lookup & Search
/lookup/id/{id}- Gene/transcript lookup/search- Gene search functionality
Sequences
/sequence/id/{id}- Feature sequences/sequence/region/{species}/{region}- Genomic sequences
Comparative Genomics
/homology/id/{id}- Homology data/genetree/id/{id}- Gene trees
Variation
/variation/region/{species}/{region}- Variant data/vep/species/{species}/region- Variant effect prediction
Regulation
/regulatory/species/{species}/region/{region}- Regulatory features/regulatory/species/{species}/microarray/{region}- Motif features
Cross-references
/xrefs/id/{id}- External database references/map/coords/{species}/{assembly}/{region}- Coordinate mapping
Information
/info/species- Available species/info/assembly/{species}- Assembly information
Support
For issues related to:
- Server functionality: Check server logs and error messages
- Ensembl data: Refer to Ensembl documentation
- API usage: See Ensembl REST API guide
Contributing
Contributions are welcome! Please ensure:
- TypeScript compliance
- Comprehensive error handling
- Documentation updates
- Test coverage for new features
Related Tools
This server integrates well with other bioinformatics MCP servers:
- UniProt Server: Protein data integration
- AlphaFold Server: 3D structure predictions
- STRING Server: Protein interaction networks
- PDB Server: Structural biology data
About Augmented Nature
This Ensembl MCP Server is developed by Augmented Nature, a company focused on building AI-powered tools for scientific research and discovery.
Citation
If you use this project in your research or publications, please cite it as follows:
author = {Moudather Chelbi},
title = {Ensembl MCP Server},
year = {2025},
howpublished = {https://github.com/Augmented-Nature/Ensembl-MCP-Server},
note = {Accessed: 2025-06-29}