Ensembl MCP Server

🚀 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

🚀 Quick Start

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 Examples

Basic Usage

Usage with Claude Desktop

Setup Instructions

1. Build the server (if not already done):

npm run build

2. 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
3. Restart Claude Desktop to load the server.

Available Tools (25 total)

• Gene & Transcript Information
  • lookup_gene - Get detailed gene information by stable ID or symbol.
  • get_transcripts - Get all transcripts for a gene with detailed structure.
  • search_genes - Search for genes by name, description, or identifier.
• Sequence Data
  • get_sequence - Get DNA sequence for genomic coordinates or gene/transcript ID.
  • get_cds_sequence - Get coding sequence (CDS) for a transcript.
  • translate_sequence - Translate DNA sequence to protein sequence.
• Comparative Genomics
  • get_homologs - Find orthologous and paralogous genes across species.
  • get_gene_tree - Get phylogenetic tree for gene family.
• Variant Data
  • get_variants - Get genetic variants in a genomic region.
  • get_variant_consequences - Predict consequences of variants on genes and transcripts.
• Regulatory Features
  • get_regulatory_features - Get regulatory elements in genomic region.
  • get_motif_features - Get transcription factor binding motifs in genomic region.
• Cross-References & Annotations
  • get_xrefs - Get external database cross-references for genes.
  • map_coordinates - Convert coordinates between genome assemblies.
• Species & Assembly Information
  • list_species - Get list of available species and assemblies.
  • get_assembly_info - Get genome assembly information and statistics.
  • get_karyotype - Get chromosome information and karyotype.
• Batch Processing
  • batch_gene_lookup - Look up multiple genes simultaneously.
  • batch_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..."

Advanced Usage

Not provided in the original document.

📚 Documentation

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 format
• 1:1000000-2000000 - Without 'chr' prefix
• ENSG00000139618 - 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

🔧 Technical Details

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 URL
• REQUEST_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

📄 License

Not provided in the original document.

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:

@misc{ensemblmcp2025, 
author = {Moudather Chelbi},
title = {Ensembl MCP Server},
year = {2025},
howpublished = {https://github.com/Augmented-Nature/Ensembl-MCP-Server},
note = {Accessed: 2025-06-29}