Can I use this for 3D protein structure analysis?

Absolutely. It includes patterns for the Bio.PDB module to parse PDB/mmCIF files, navigate the SMCRA hierarchy, and calculate atomic distances or RMSD.

Does this skill support the latest Biopython version?

Yes, this skill is optimized for Biopython 1.85 (released January 2025) and supports Python 3 environments.

Is it efficient for large genomic files?

Yes, the skill emphasizes the use of iterators like SeqIO.parse to process large FASTA or FASTQ files without exhausting system memory.

How does it handle NCBI database rate limits?

The skill provides implementation patterns for Bio.Entrez that include mandatory email configuration and API key usage to ensure compliance with NCBI rate limits.

Biopython Bioinformatics Toolkit

Name: Biopython Bioinformatics Toolkit
Author: Microck

byMicrock

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数据科学与机器学习

Provides specialized tools for biological computation, sequence analysis, and programmatic access to NCBI databases using Biopython.

关于

This skill equips Claude with specialized knowledge of the Biopython library (version 1.85+) to streamline computational molecular biology tasks. It enables efficient sequence manipulation (DNA/RNA/Protein), high-throughput file parsing for formats like FASTA and GenBank, structural analysis via PDB files, and automated NCBI data retrieval through Entrez. Whether performing sequence alignments, building phylogenetic trees, or running BLAST workflows, this skill provides the specific implementation patterns and best practices needed for robust bioinformatics development.

主要功能

Sequence alignment modules for pairwise and multiple sequence analysis using substitution matrices
Comprehensive sequence manipulation and file I/O for FASTA, FASTQ, and GenBank formats
81 GitHub stars
Programmatic access to NCBI databases via Bio.Entrez with automated rate-limiting support
Phylogenetic tree construction, manipulation, and visualization workflows
Structural bioinformatics tools for parsing and analyzing 3D protein structures (PDB/mmCIF)

使用场景

Automating the retrieval and processing of genomic sequences and metadata from NCBI GenBank
Developing pipelines for protein structure analysis and RMSD calculation from PDB data
Building and visualizing phylogenetic trees from multiple sequence alignment (MSA) data

关于

主要功能

Sequence alignment modules for pairwise and multiple sequence analysis using substitution matrices
Comprehensive sequence manipulation and file I/O for FASTA, FASTQ, and GenBank formats
81 GitHub stars
Programmatic access to NCBI databases via Bio.Entrez with automated rate-limiting support
Phylogenetic tree construction, manipulation, and visualization workflows
Structural bioinformatics tools for parsing and analyzing 3D protein structures (PDB/mmCIF)

使用场景

Automating the retrieval and processing of genomic sequences and metadata from NCBI GenBank
Developing pipelines for protein structure analysis and RMSD calculation from PDB data
Building and visualizing phylogenetic trees from multiple sequence alignment (MSA) data