bioinformatics-mcp-server

Bioinformatics data for AI agents — gene search, protein structures, clinical variants, PubMed literature, and DNA sequences via NCBI and UniProt. No API key required.

GitHub

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.

PyPI version License: MIT

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)

ToolWhat it does
search_genesSearch genes by symbol, name, or function
get_gene_detailsFull gene info by NCBI Gene ID
search_clinvar_variantsClinical variants and mutations
get_taxonomyTaxonomic classification of organisms
get_ncbi_sequenceDNA/protein sequences (FASTA/GenBank)

UniProt (2 tools)

ToolWhat it does
search_proteinsSearch proteins by name, gene, or organism
get_protein_detailsProtein details by UniProt accession

PubMed (3 tools)

ToolWhat it does
search_pubmedSearch biomedical literature
get_pubmed_abstractFull abstract of a PubMed article
get_pubmed_citationsArticles citing a specific publication

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License

MIT

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