Can this skill help with NCBI database access?

Yes, it includes optimized patterns for using Bio.Entrez to search and fetch records from PubMed, GenBank, and Protein databases while adhering to NCBI's rate limits.

How does it handle different biological file formats?

The skill facilitates the use of SeqIO and AlignIO to read, write, and convert between numerous formats including FASTA, GenBank, FASTQ, Phylip, and Nexus.

What is the Biopython Claude Code Skill?

It is a specialized domain skill that provides Claude with the best practices and code patterns needed to use the Biopython library for molecular biology and bioinformatics tasks.

Does it support protein structure analysis?

Absolutely. It provides guidance on using the Bio.PDB module to parse PDB/mmCIF files, navigate molecular hierarchies, and calculate structural distances.

Biopython Bioinformatics

Name: Biopython Bioinformatics
Author: Microck

byMicrock

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Data Science & ML

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

About

The Biopython skill equips Claude with specialized knowledge for computational molecular biology, providing structured guidance and implementation patterns for the industry-standard Biopython toolkit. It enables Claude to efficiently handle biological data workflows including sequence manipulation, programmatic access to NCBI databases via Entrez, parsing of complex file formats like FASTA and PDB, and advanced phylogenetics. This skill is ideal for researchers and developers building reproducible bioinformatics pipelines, performing genomic analysis, or exploring structural biology within the Python ecosystem.

Key Features

Comprehensive parsing and conversion of FASTA, GenBank, FASTQ, and PDB file formats.
Programmatic access to NCBI/PubMed databases via Bio.Entrez with rate-limit management.
Automated BLAST workflows for remote and local sequence alignment and result parsing.
81 GitHub stars
Structural bioinformatics tools for 3D protein analysis and RMSD calculation.
Advanced sequence manipulation including translation, transcription, and motif analysis.

Use Cases

Building automated pipelines to fetch, filter, and translate genomic sequences from GenBank.
Performing high-throughput BLAST searches and extracting top hits for comparative genomics.
Constructing and visualizing phylogenetic trees from multiple sequence alignments.

About

Key Features

Comprehensive parsing and conversion of FASTA, GenBank, FASTQ, and PDB file formats.
Programmatic access to NCBI/PubMed databases via Bio.Entrez with rate-limit management.
Automated BLAST workflows for remote and local sequence alignment and result parsing.
81 GitHub stars
Structural bioinformatics tools for 3D protein analysis and RMSD calculation.
Advanced sequence manipulation including translation, transcription, and motif analysis.

Use Cases

Building automated pipelines to fetch, filter, and translate genomic sequences from GenBank.
Performing high-throughput BLAST searches and extracting top hits for comparative genomics.
Constructing and visualizing phylogenetic trees from multiple sequence alignments.