How does the skill handle NCBI rate limits?

The skill follows Biopython best practices by requiring an email address for Entrez identification and encouraging the use of handles to manage network resources efficiently.

Can I use this skill for protein structure analysis?

Yes, it includes full support for Bio.PDB, allowing you to parse structure files, navigate the SMCRA hierarchy, and calculate structural metrics like RMSD.

Which biological file formats are supported?

This skill supports most common bioinformatics formats including FASTA, GenBank, FASTQ, PDB, mmCIF, Newick, and NEXUS.

Does this skill require an NCBI API key?

An API key is not strictly required, but it is highly recommended for higher rate limits (10 requests/second instead of 3) when performing frequent Bio.Entrez queries.

Biopython Molecular Biology Toolkit

Name: Biopython Molecular Biology Toolkit
Author: ovachiever

byovachiever

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Data Science & ML

Performs advanced computational molecular biology tasks including sequence analysis, database queries, and structural bioinformatics.

About

This skill empowers Claude to handle complex bioinformatics workflows by leveraging the comprehensive Biopython library. It provides a standardized framework for manipulating biological sequences, parsing specialized file formats like FASTA and GenBank, and programmatically accessing NCBI databases via Entrez. Whether you are automating BLAST searches, analyzing 3D protein structures from PDB files, or constructing phylogenetic trees, this skill provides the domain-specific logic and best practices needed to ensure biological accuracy and efficient data processing within your development environment.

Key Features

Structural bioinformatics tools for parsing and analyzing PDB and mmCIF files
Sequence manipulation, translation, and transcription across various biological formats
Automated BLAST search execution and XML result parsing
5 GitHub stars
Programmatic access to NCBI databases including PubMed, GenBank, and Protein
Phylogenetic tree manipulation, distance calculation, and visualization

Use Cases

Automating the retrieval and processing of genomic sequences for large-scale studies
Building automated pipelines for sequence alignment and phylogenetic tree construction
Analyzing protein structure hierarchies and calculating residue distances or bond angles

About

Key Features

Structural bioinformatics tools for parsing and analyzing PDB and mmCIF files
Sequence manipulation, translation, and transcription across various biological formats
Automated BLAST search execution and XML result parsing
5 GitHub stars
Programmatic access to NCBI databases including PubMed, GenBank, and Protein
Phylogenetic tree manipulation, distance calculation, and visualization

Use Cases

Automating the retrieval and processing of genomic sequences for large-scale studies
Building automated pipelines for sequence alignment and phylogenetic tree construction
Analyzing protein structure hierarchies and calculating residue distances or bond angles