# 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](https://badge.fury.io/py/bioinformatics-mcp-server.svg)](https://pypi.org/project/bioinformatics-mcp-server/)
[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)

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

## Quick Start

```bash
pip install bioinformatics-mcp-server
```

```json
{
  "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](https://pypi.org/project/medical-data-mcp-server/) — WHO health data
- [crossref-academic-mcp-server](https://pypi.org/project/crossref-academic-mcp-server/) — Academic papers via Crossref

## License

MIT