How does this skill handle NCBI rate limits?

The skill provides patterns for configuring Entrez.email and using API keys to ensure your programmatic queries comply with NCBI's usage policies and rate limits.

Can I use this for protein structure analysis?

Yes, it includes specialized documentation for Bio.PDB to help you navigate structural hierarchies (SMCRA) and calculate distances or secondary structures.

Which sequence file formats are supported?

The skill supports all major bioinformatics formats including FASTA, GenBank, FASTQ, Clustal, Phylip, and mmCIF via Bio.SeqIO and Bio.AlignIO.

Does this skill require external Python libraries?

Yes, implementation requires Biopython and NumPy. The skill provides the specific code snippets needed to install and configure these dependencies correctly.

Biopython Molecular Biology Toolkit

Name: Biopython Molecular Biology Toolkit
Author: Activer007

byActiver007

0•

Data Science & ML

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

The Biopython skill equips Claude with specialized expertise in bioinformatics and computational biology. It provides a comprehensive set of tools for manipulating biological sequences, parsing complex file formats like FASTA and PDB, and interacting programmatically with NCBI's Entrez databases. Whether you are performing sequence alignments, running BLAST searches, or analyzing 3D protein structures, this skill ensures Claude follows best practices for biological data science, including proper rate limiting and modular Python implementation patterns.

Key Features

01Phylogenetic tree construction, manipulation, and visualization

02Sequence manipulation and translation for DNA, RNA, and proteins

03Parsing and conversion of biological formats (FASTA, GenBank, FASTQ, PDB)

04Programmatic NCBI database access via Bio.Entrez with automated rate limiting

05Structural bioinformatics for analyzing 3D protein models and hierarchies

060 GitHub stars

Use Cases

01Automating the retrieval and analysis of genomic sequences from GenBank

02Setting up BLAST search pipelines and parsing results for homology studies

03Calculating structural metrics like RMSD and atomic distances in protein models

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