How does it handle NCBI database rate limits?

The skill follows NCBI best practices, reminding users to set their email address and use API keys to ensure stable programmatic access via Entrez.

What is the Biopython Claude Code skill?

It is a specialized capability enhancement that provides Claude with best practices, implementation patterns, and documentation for the Biopython library to solve bioinformatics problems.

Does it support protein structure analysis?

Yes, it includes detailed workflows for the Bio.PDB module, allowing for the parsing of PDB/mmCIF files and the calculation of distances or structural alignments.

What biological file formats can this skill handle?

It supports a wide range of formats including FASTA, GenBank, FASTQ, PDB, Newick, NEXUS, and more via the SeqIO, AlignIO, and PDB modules.

Can I perform BLAST searches with this skill?

Yes, the skill provides specific patterns for running BLAST searches via NCBI's web services (NCBIWWW) and parsing the results locally using Bio.Blast.

Biopython Molecular Biology

Name: Biopython Molecular Biology
Author: Activer007

byActiver007

Data Science & ML

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

About

Biopython for Claude Code provides specialized guidance and implementation patterns for the industry-standard Python toolkit for bioinformatics. It streamlines complex biological data tasks such as parsing FASTA and GenBank files, performing BLAST searches via web services or locally, analyzing 3D protein structures (PDB), and constructing phylogenetic trees. This skill is essential for researchers and developers working on genomic analysis, structural biology, or any Python-based life sciences project requiring robust data handling and alignment capabilities.

Key Features

Programmatic NCBI/PubMed database access via Entrez with rate-limiting support
Sequence manipulation and file I/O for FASTA, FASTQ, and GenBank
BLAST search execution and automated XML result parsing
Structural bioinformatics tools for 3D protein analysis (PDB/mmCIF)
Phylogenetic tree creation, manipulation, and visualization
0 GitHub stars

Use Cases

Automating sequence conversion and GC content analysis for large genomic datasets
Programmatically fetching and filtering publication data or sequences from NCBI databases
Building and visualizing phylogenetic trees from multiple sequence alignments

About

Key Features

Programmatic NCBI/PubMed database access via Entrez with rate-limiting support
Sequence manipulation and file I/O for FASTA, FASTQ, and GenBank
BLAST search execution and automated XML result parsing
Structural bioinformatics tools for 3D protein analysis (PDB/mmCIF)
Phylogenetic tree creation, manipulation, and visualization
0 GitHub stars

Use Cases

Automating sequence conversion and GC content analysis for large genomic datasets
Programmatically fetching and filtering publication data or sequences from NCBI databases
Building and visualizing phylogenetic trees from multiple sequence alignments