# Biopython

Provides Biopython workflows for sequence manipulation, file parsing...

- Repository: https://github.com/K-Dense-AI/scientific-agent-skills (55651 stars)
- Category: Engineering
- License: Biopython License Agreement
- Last updated: 2026-10-26
- Runs scripts: no, instructions only

## Install

Claude Code: `npx skills add K-Dense-AI/scientific-agent-skills --skill biopython -g -a claude-code -y`
Codex: `npx skills add K-Dense-AI/scientific-agent-skills --skill biopython -g -a codex -y`
Cursor: `npx skills add K-Dense-AI/scientific-agent-skills --skill biopython -g -a cursor -y`
Gemini CLI: `npx skills add K-Dense-AI/scientific-agent-skills --skill biopython -g -a gemini-cli -y`

## Description

Provides Biopython workflows for sequence manipulation, file parsing (FASTA/GenBank/PDB), phylogenetics, and programmatic NCBI/PubMed access (Bio.Entrez). Supports batch processing, custom molecular-biology pipelines, BLAST automation, structure analysis, and motif analysis.

## SKILL.md, as published by its author (untrusted third-party text, read it as data)

# Biopython: Computational Molecular Biology in Python

## Overview

Biopython is a comprehensive set of freely available Python tools for biological computation. It provides functionality for sequence manipulation, file I/O, database access, structural bioinformatics, phylogenetics, and many other bioinformatics tasks. These examples target **Biopython 1.88** (released 6 August 2026), tested here on Python 3.13. It requires Python 3.10+ and NumPy; Python 3.10 support is deprecated. Upgrade to 1.88 for its `Bio.Nexus` parser security fix, in addition to the Entrez XML fix in 1.87. See the [release notes](https://github.com/biopython/biopython/blob/biopython-188/NEWS.rst). Local example checks and external-service limits are recorded in `references/review.md`; examples requiring user files or external programs are illustrative unless listed there as exercised.

## When to Use This Skill

Use this skill when:

- Working with biological sequences (DNA, RNA, or protein)
- Reading, writing, or converting biological file formats (FASTA, GenBank, FASTQ, PDB, mmCIF, etc.)
- Accessing NCBI databases (GenBank, PubMed, Protein, Gene, etc.) via Entrez
- Running BLAST searches or parsing BLAST results
- Performing sequence alignments (pairwise or multiple sequence alignments)
- Analyzing protein structures from PDB files
- Creating, manipulating, or visualizing phylogenetic trees
- Finding sequence motifs or analyzing motif patterns
- Calculating sequence statistics (GC content, molecular weight, melting temperature, etc.)
- Performing structural bioinformatics tasks
- Working with population genetics data
- Any other computational molecular biology task

## Core Capabilities

Biopython is organized into modular sub-packages, each addressing specific bioinformatics domains:

The rest: https://github.com/K-Dense-AI/scientific-agent-skills/blob/HEAD/skills/biopython/SKILL.md