What biological file formats does this skill support?

The Biopython skill supports all major bioinformatics formats including FASTA, GenBank, FASTQ, PDB, mmCIF, Clustal, and Phylip for both reading and writing.

Are there specific requirements for accessing NCBI databases?

When using the Entrez module for database access, NCBI requires you to provide a valid email address. This skill helps you set up those parameters correctly.

Can I use this skill to search PubMed or GenBank?

Yes, it includes specialized patterns for using Bio.Entrez to perform programmatic searches, fetch records, and download sequences from NCBI databases.

Does it support protein structure analysis?

Yes, the skill provides implementation guidance for Bio.PDB, allowing you to parse structures, navigate atom hierarchies, and calculate distances or RMSD.

Biopython Molecular Biology Toolkit

Name: Biopython Molecular Biology Toolkit
Author: Activer007

byActiver007

0•

Data Science & ML

Simplifies computational molecular biology tasks including sequence manipulation, phylogenetic analysis, and programmatic NCBI database access.

This Claude Code Skill integrates the comprehensive Biopython library into your AI development workflow, enabling advanced biological computation and bioinformatics analysis. It provides specialized patterns for handling DNA, RNA, and protein sequences, parsing complex file formats like FASTA and GenBank, and executing programmatic queries against NCBI databases via Entrez. Whether you are running BLAST searches, analyzing protein structures from PDB files, or constructing phylogenetic trees, this skill provides domain-specific guidance and implementation patterns to ensure accurate and efficient scientific computing.

Key Features

01Advanced biological sequence manipulation, translation, and statistics

020 GitHub stars

03Automated BLAST workflow execution and XML result parsing

04Phylogenetic tree construction and structural bioinformatics tools

05Comprehensive parsing for FASTA, GenBank, FASTQ, and PDB file formats

06Programmatic NCBI database access via Entrez (PubMed, Gene, Protein)

Use Cases

01Building and visualizing phylogenetic trees from multiple sequence alignments

02Fetching and processing genomic data and research publications from NCBI

03Automating high-throughput sequence analysis pipelines and format conversions

What are Skills?·How to Install

Install with 🐟 Skill.Fish

npx skillfish add activer007/ordinary-claude-skills biopython

For use in Claude.ai and ChatGPT

Download Skill