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

Data Science & ML

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

About

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

Phylogenetic tree construction, manipulation, and visualization
Sequence manipulation and translation for DNA, RNA, and proteins
Parsing and conversion of biological formats (FASTA, GenBank, FASTQ, PDB)
Programmatic NCBI database access via Bio.Entrez with automated rate limiting
Structural bioinformatics for analyzing 3D protein models and hierarchies
0 GitHub stars

Use Cases

Automating the retrieval and analysis of genomic sequences from GenBank
Setting up BLAST search pipelines and parsing results for homology studies
Calculating structural metrics like RMSD and atomic distances in protein models

About

Key Features

Phylogenetic tree construction, manipulation, and visualization
Sequence manipulation and translation for DNA, RNA, and proteins
Parsing and conversion of biological formats (FASTA, GenBank, FASTQ, PDB)
Programmatic NCBI database access via Bio.Entrez with automated rate limiting
Structural bioinformatics for analyzing 3D protein models and hierarchies
0 GitHub stars

Use Cases

Automating the retrieval and analysis of genomic sequences from GenBank
Setting up BLAST search pipelines and parsing results for homology studies
Calculating structural metrics like RMSD and atomic distances in protein models