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biopython

Computational molecular biology library (sequence I/O, alignment, phylogenetics). Input: FASTA/GenBank/PDB files you already have. Output: parsed sequences, alignments, phylogenetic trees, structural analysis. Does NOT search databases — invoking by topic returns only a placeholder stub. For literature use pubmed, for protein lookup use uniprot, for sequence homology use blast.

skills/biopython/SKILL.md

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Oct 30, 2026
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Apache-2.0

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# Biopython: Computational Molecular Biology in Python

## ⚠<U+FE0F> When NOT To Use This Skill

**Do NOT invoke biopython** if you want to:
- Search literature about a topic (e.g. "KRAS covalent inhibitors") → use **pubmed**
- Look up a protein by name or accession → use **uniprot**
- Find compounds or chemical data → use **pubchem** or **chembl**
- Run a BLAST sequence search → use the **blast** skill

**The biopython `demo.py` script returns only a placeholder message** — it contains no actual scientific data. It exists to confirm the library is installed. Real biopython usage requires writing Python code that operates on sequence files you provide.

**Correct agent workflow:**
1. Retrieve a sequence accession from uniprot or NCBI (e.g. `P01116` for KRAS)