What is the Biopython Claude Code Skill?

It is a specialized plugin for Claude that provides optimized code patterns and domain-specific guidance for performing bioinformatics and molecular biology tasks using the Biopython library.

Can I analyze protein structures with this skill?

Absolutely. It provides tools for parsing PDB and mmCIF files, navigating the SMCRA hierarchy, and performing structural calculations like distance and RMSD.

Which Python version is supported?

The skill is optimized for Biopython 1.85 (released January 2025) and requires Python 3 and NumPy.

How does the skill handle large biological datasets?

It promotes best practices like using iterators (e.g., SeqIO.parse) to process large FASTA or FASTQ files efficiently without overloading system memory.

Does this skill support NCBI database queries?

Yes, it includes robust patterns for using Bio.Entrez to search and download data from PubMed, GenBank, and other NCBI databases while respecting rate limits.

Biopython Molecular Biology

Name: Biopython Molecular Biology
Author: x-cmd

byx-cmd

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Ciencia de Datos y ML

Performs advanced biological computation and molecular biology workflows using the Biopython toolkit.

Acerca de

This skill empowers Claude to handle complex bioinformatics tasks by providing specialized implementation patterns for the Biopython library. It streamlines biological sequence manipulation, file parsing for major formats like FASTA and GenBank, and programmatic access to NCBI databases via Entrez. Whether you are performing protein structure analysis, constructing phylogenetic trees, or orchestrating BLAST searches, this skill ensures that generated code adheres to domain-specific best practices, proper rate-limiting, and memory-efficient data handling.

Características Principales

Biological sequence manipulation, translation, and reverse complementation
Programmatic NCBI database access with Entrez API integration
Structural bioinformatics tools for PDB parsing and RMSD calculations
8 GitHub stars
Phylogenetic tree construction and visualization workflows
Parsing and conversion of bioinformatics file formats (FASTA, GenBank, FASTQ, PDB)

Casos de Uso

Automating the retrieval and analysis of genomic sequences from GenBank
Analyzing 3D protein structures to calculate residue distances and identify motifs
Developing high-throughput BLAST search pipelines with automated result parsing

Acerca de

Características Principales

Biological sequence manipulation, translation, and reverse complementation
Programmatic NCBI database access with Entrez API integration
Structural bioinformatics tools for PDB parsing and RMSD calculations
8 GitHub stars
Phylogenetic tree construction and visualization workflows
Parsing and conversion of bioinformatics file formats (FASTA, GenBank, FASTQ, PDB)

Casos de Uso

Automating the retrieval and analysis of genomic sequences from GenBank
Analyzing 3D protein structures to calculate residue distances and identify motifs
Developing high-throughput BLAST search pipelines with automated result parsing