MCP server for the gget bioinformatics library
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 termsgget_info: Fetch detailed information for Ensembl IDsgget_seq: Retrieve nucleotide or amino acid sequencesgget_ref: Get reference genome information from Ensembl
Sequence Analysis
gget_blast: BLAST nucleotide or amino acid sequencesgget_blat: Find genomic locations of sequencesgget_muscle: Align multiple sequences
Expression & Functional Analysis
gget_archs4: Get gene expression data from ARCHS4gget_enrichr: Perform gene set enrichment analysis
Protein Structure & Function
gget_pdb: Fetch protein structure data from PDBgget_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)
# Download and install uv
curl -LsSf https://astral.sh/uv/install.sh | sh
# Verify installation
uv --version
uvx --version
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 reposi
Tools (13)
gget_searchFind Ensembl IDs associated with search termsgget_infoFetch detailed information for Ensembl IDsgget_seqRetrieve nucleotide or amino acid sequencesgget_refGet reference genome information from Ensemblgget_blastBLAST nucleotide or amino acid sequencesgget_blatFind genomic locations of sequencesgget_muscleAlign multiple sequencesgget_archs4Get gene expression data from ARCHS4gget_enrichrPerform gene set enrichment analysisgget_pdbFetch protein structure data from PDBgget_alphafoldPredict protein structure using AlphaFoldgget_cosmicSearch COSMIC database for cancer mutationsgget_cellxgeneQuery single-cell RNA-seq data from CellxGeneConfiguration
{
"mcpServers": {
"gget-mcp": {
"command": "uvx",
"args": ["gget-mcp"]
}
}
}