longevity-genie/gget-mcp

MCP (Model Context Protocol) server for the gget bioinformatics library.
This server implements the Model Context Protocol (MCP) for gget, providing a standardized interface for accessing powerful bioinformatics tools and databases. MCP enables AI assistants and agents to perform complex genomics queries through structured interfaces.
The gget bioinformatics toolkit provides efficient querying of genomic databases and includes functions for:
- Gene and sequence information retrieval
- BLAST and sequence alignment
- Protein structure prediction
- Gene expression analysis
- Functional enrichment analysis
- And much more!
🚀 Quick Example: What Can You Do?
See how the gget MCP server works in practice with AI assistants
**👤 User:** "Analyze the TP53 gene - find its details and protein sequence, then check for cancer mutations"
**🤖 AI Assistant:** I'll help you analyze TP53 step by step:
*[Uses gget_search]* → Found TP53 (ENSG00000141510) on chromosome 17
*[Uses gget_info]* → TP53 is a protein-coding tumor suppressor gene
*[Uses gget_seq with translate=True]* → Retrieved 393 amino acid protein sequence
*[Uses gget_cosmic]* → Found hotspot mutations R175H, R248Q, R273H in multiple cancers
**👤 User:** "Now predict the 3D structure of this protein sequence: MSKGEELFTGVVPILVEL..."
**🤖 AI Assistant:** Let me analyze this sequence:
*[Uses gget_blast]* → Identified as Green Fluorescent Protein (GFP)
*[Uses gget_alphafold]* → Predicted classic beta-barrel structure with 90%+ confidence
**👤 User:** "Perform pathway enrichment for DNA repair genes: TP53, BRCA1, BRCA2, ATM"
**🤖 AI Assistant:** *[Uses gget_enrichr]* → Top pathways: DNA Damage Response, Homologous Recombination, Cell Cycle Checkpoints, p53 Signaling
**See how powerful this is?** You can now ask natural language questions about genes, sequences, mutations, and pathways - the AI does the complex bioinformatics work for you!
About MCP (Model Context Protocol)
Learn more about the Model Context Protocol
MCP is a protocol that bridges the gap between AI systems and specialized domain tools. It enables:
- **Structured Access**: Direct connection to powerful bioinformatics tools and databases
- **Natural Language Queries**: Simplified interaction with complex genomics workflows
- **Type Safety**: Strong typing and validation through FastMCP
- **AI Integration**: Seamless integration with AI assistants and agents
If you want to understand more about what the Model Context Protocol is and how to use it more efficiently, you can take the DeepLearning AI Course or search for MCP videos on YouTube.
Available Tools
Comprehensive bioinformatics functionality through gget
Gene Information & Search
- **gget_search**: Find Ensembl IDs associated with search terms
- **gget_info**: Fetch detailed information for Ensembl IDs
- **gget_seq**: Retrieve nucleotide or amino acid sequences
- **gget_ref**: Get reference genome information from Ensembl
Sequence Analysis
- **gget_blast**: BLAST nucleotide or amino acid sequences
- **gget_blat**: Find genomic locations of sequences
- **gget_muscle**: Align multiple sequences
Expression & Functional Analysis
- **gget_archs4**: Get gene expression data from ARCHS4
- **gget_enrichr**: Perform gene set enrichment analysis
Protein Structure & Function
- **gget_pdb**: Fetch protein structure data from PDB
- **gget_alphafold**: Predict protein structure using AlphaFold
Cancer & Mutation Analysis
- **gget_cosmic**: Search COSMIC database for cancer mutations
Single-cell Analysis
- **gget_cellxgene**: Query single-cell RNA-seq data from CellxGene
Quick Start
Installing uv (optional - uvx can auto-install)
uvx is a very nice tool that can run a python package installing it if needed.
Running with uvx
You can run the gget-mcp server directly using uvx without cloning the repository:
Other uvx modes (STDIO, HTTP, SSE)
STDIO Mode (for MCP clients that require stdio)
HTTP Mode (Web Server)
SSE Mode (Server-Sent Events)
In cases when there are problems with uvx often they can be caused by cleaning uv cache:
The HTTP mode will start a web server that you can access at http://localhost:3002/mcp (with documentation at http://localhost:3002/docs). The STDIO mode is designed for MCP clients that communicate via standard input/output, while SSE mode uses Server-Sent Events for real-time communication.