Can this skill analyze protein structures?

Yes, it includes patterns for Bio.PDB to parse PDB/mmCIF files, navigate the SMCRA hierarchy, and perform structural calculations like atomic distances.

What version of Biopython is supported?

The skill is updated for Biopython 1.85 (released Jan 2025), supporting Python 3 and requiring NumPy for numerical operations.

What is the Biopython Claude Code skill?

It is a specialized capability that provides Claude with domain-specific guidance, best practices, and implementation patterns for the Biopython library used in molecular biology.

How does this skill handle NCBI database access?

It uses the Bio.Entrez module with optimized patterns for searching and fetching data, including mandatory email identification and API key support for higher rate limits.

Does it support phylogenetic tree visualization?

Yes, it provides code patterns for Bio.Phylo to read, manipulate, and visualize trees in formats like Newick, NEXUS, and phyloXML.

Biopython Bioinformatics Tools

Name: Biopython Bioinformatics Tools
Author: ricable

byricable

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Data Science & ML

Streamlines computational molecular biology tasks and bioinformatics workflows using the Biopython library.

About

The Biopython skill equips Claude with specialized patterns for biological computation, enabling complex tasks such as DNA/RNA/protein sequence manipulation, structural analysis of protein files, and phylogenetic tree construction. It provides optimized workflows for programmatic access to NCBI databases via Entrez, automated BLAST searches, and parsing of industry-standard file formats like FASTA, GenBank, and PDB. This skill is ideal for researchers and developers building agentic bioinformatics pipelines that require high-precision data handling and scientific accuracy.

Key Features

Comprehensive sequence manipulation including translation, transcription, and reverse complement
Programmatic NCBI database access via Bio.Entrez for sequence and publication retrieval
Structural bioinformatics tools for protein 3D analysis and RMSD calculation
Phylogenetic tree manipulation, visualization, and consensus building
1 GitHub stars
Parsing and conversion for biological file formats (FASTA, GenBank, FASTQ, PDB, mmCIF)

Use Cases

Automating large-scale sequence retrieval and analysis from GenBank or PubMed
Creating phylogenetic trees from multiple sequence alignments for evolutionary studies
Developing pipelines for protein structure analysis and molecular distance calculations

About

Key Features

Comprehensive sequence manipulation including translation, transcription, and reverse complement
Programmatic NCBI database access via Bio.Entrez for sequence and publication retrieval
Structural bioinformatics tools for protein 3D analysis and RMSD calculation
Phylogenetic tree manipulation, visualization, and consensus building
1 GitHub stars
Parsing and conversion for biological file formats (FASTA, GenBank, FASTQ, PDB, mmCIF)

Use Cases

Automating large-scale sequence retrieval and analysis from GenBank or PubMed
Creating phylogenetic trees from multiple sequence alignments for evolutionary studies
Developing pipelines for protein structure analysis and molecular distance calculations