biopython
Comprehensive molecular biology toolkit. Use for sequence manipulation, file parsing (FASTA/GenBank/PDB), phylogenetics, and programmatic NCBI/PubMed access (Bio.Entrez). Best for batch processing, custom bioinformatics pipelines, BLAST automation. For quick lookups use gget; for multi-service integration use bioservices.
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---
name: biopython
description: Comprehensive molecular biology toolkit. Use for sequence manipulation, file parsing (FASTA/GenBank/PDB), phylogenetics, and programmatic NCBI/PubMed access (Bio.Entrez). Best for batch processing, custom bioinformatics pipelines, BLAST automation. For quick lookups use gget; for multi-service integration use bioservices.
license: Unknown
metadata:
skill-author: K-Dense Inc.
---
# Biopython: Computational Molecular Biology in Python
## Overview
Biopython iHow to Use
Recommended: Install to project (local)
mkdir -p .claude/skills
curl -o .claude/skills/biopython.md \
https://raw.githubusercontent.com/K-Dense-AI/claude-scientific-skills/main/scientific-skills/biopython/SKILL.mdSkill is scoped to this project only. Add .claude/skills/ to your .gitignoreif you don't want to commit it.
Alternative: Clone full repo
git clone https://github.com/K-Dense-AI/claude-scientific-skillsThen reference at scientific-skills/biopython/SKILL.md
Related Skills
biopython
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.
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gget
Fast CLI/Python queries to 20+ bioinformatics databases. Use for quick lookups: gene info, BLAST searches, AlphaFold structures, enrichment analysis. Best for interactive exploration, simple queries. For batch processing or advanced BLAST use biopython; for multi-database Python workflows use bioservices.
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Direct REST API access to PubMed. Advanced Boolean/MeSH queries, E-utilities API, batch processing, citation management. For Python workflows, prefer biopython (Bio.Entrez). Use this for direct HTTP/REST work or custom API implementations.
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bioservices
Unified Python interface to 40+ bioinformatics services. Use when querying multiple databases (UniProt, KEGG, ChEMBL, Reactome) in a single workflow with consistent API. Best for cross-database analysis, ID mapping across services. For quick single-database lookups use gget; for sequence/file manipulation use biopython.
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by K-Dense-AI · claude-scientific-skills