Can I process large FASTA or FASTQ files with this skill?

Yes, it implements memory-efficient patterns using SeqIO.parse iterators, which allow you to process large genomic datasets one record at a time without exhausting system memory.

How do I perform sequence alignments using this skill?

The skill provides patterns for both pairwise alignment using Bio.Align and handling multiple sequence alignments through Bio.AlignIO, supporting standard formats like Clustal and Phylip.

Can I run BLAST searches directly through Claude?

Yes, it supports Bio.Blast for running remote searches via NCBI's web services and parsing the resulting XML output into readable Python objects.

How does this skill handle NCBI database queries?

The skill uses the Bio.Entrez module to programmatically search and fetch data from NCBI databases like PubMed and GenBank, incorporating required parameters like email and API keys for optimal rate limits.

Does Biopython support 3D protein structure analysis?

Yes, it includes the Bio.PDB module for parsing PDB and mmCIF files, navigating the SMCRA (Structure/Model/Chain/Residue/Atom) hierarchy, and calculating distances or RMSD.

Biopython Bioinformatics Toolkit

Name: Biopython Bioinformatics Toolkit
Author: Activer007

byActiver007

Ciencia de Datos y ML

Facilitates computational molecular biology tasks using the Biopython library for sequence analysis, structural bioinformatics, and NCBI database integration.

Acerca de

The Biopython skill provides a comprehensive environment for biological computation, enabling researchers and developers to perform complex bioinformatics tasks directly within Claude Code. It offers specialized guidance for sequence manipulation, parsing standard biological file formats (FASTA, GenBank, PDB), and programmatic access to NCBI databases via Entrez. Whether you are conducting phylogenetic analysis, automating BLAST workflows, or performing structural protein analysis, this skill implements domain-specific best practices and memory-efficient patterns for scientific computing.

Características Principales

Comprehensive sequence manipulation and translation via Bio.Seq
Programmatic NCBI Entrez access for automated database queries
Phylogenetic tree construction, manipulation, and visualization
0 GitHub stars
High-performance biological file I/O for FASTA, GenBank, and FASTQ
Structural bioinformatics tools for parsing and analyzing PDB files

Casos de Uso

Automating the retrieval, parsing, and translation of genomic sequences from GenBank
Analyzing protein structures and calculating molecular distances from PDB data
Building and visualizing phylogenetic trees from multiple sequence alignments

Acerca de

Características Principales

Comprehensive sequence manipulation and translation via Bio.Seq
Programmatic NCBI Entrez access for automated database queries
Phylogenetic tree construction, manipulation, and visualization
0 GitHub stars
High-performance biological file I/O for FASTA, GenBank, and FASTQ
Structural bioinformatics tools for parsing and analyzing PDB files

Casos de Uso

Automating the retrieval, parsing, and translation of genomic sequences from GenBank
Analyzing protein structures and calculating molecular distances from PDB data
Building and visualizing phylogenetic trees from multiple sequence alignments