bioinformatics-mcp-server

Bioinformatics and life science data for AI agents — gene search, protein structures, clinical variants, PubMed literature, and DNA sequences via NCBI and UniProt.

No API key required. 10 tools covering 6 data sources (NCBI Gene, ClinVar, Taxonomy, PubMed, Sequences, UniProt).

Quick Start

pip install bioinformatics-mcp-server

{
  "mcpServers": {
    "bioinformatics": {
      "command": "uvx",
      "args": ["bioinformatics-mcp-server"]
    }
  }
}

What Can You Do?

Ask your AI agent things like:

• "Search for genes related to breast cancer"
• "What clinical variants are known for BRCA1?"
• "Find recent PubMed papers about CRISPR gene editing"
• "Get the protein structure of human insulin from UniProt"
• "What species does this organism belong to?"

10 Tools

NCBI (5 tools)

Tool	What it does
search_genes	Search genes by symbol, name, or function
get_gene_details	Full gene info by NCBI Gene ID
search_clinvar_variants	Clinical variants and mutations
get_taxonomy	Taxonomic classification of organisms
get_ncbi_sequence	DNA/protein sequences (FASTA/GenBank)

UniProt (2 tools)

Tool	What it does
search_proteins	Search proteins by name, gene, or organism
get_protein_details	Protein details by UniProt accession

PubMed (3 tools)

Tool	What it does
search_pubmed	Search biomedical literature
get_pubmed_abstract	Full abstract of a PubMed article
get_pubmed_citations	Articles citing a specific publication

Related Servers

• medical-data-mcp-server — WHO health data
• crossref-academic-mcp-server — Academic papers via Crossref

License

MIT