Can I perform BLAST searches using this Biopython skill?

Yes, the skill provides guidance on running remote BLAST searches via NCBI web services and parsing the resulting XML data using Bio.Blast.

Does this skill support structural biology formats like PDB?

Absolutely. It includes comprehensive patterns for using the Bio.PDB module to parse, navigate, and analyze 3D protein structures.

Can it convert between FASTA and GenBank formats?

Yes, it utilizes Bio.SeqIO to efficiently read, write, and convert between dozens of common biological file formats.

How does this skill handle NCBI rate limits?

The skill enforces best practices such as setting Entrez.email and recommending API keys to manage rate limits and ensure stable database access.

Biopython for Bioinformatics

Name: Biopython for Bioinformatics
Author: lifangda

bylifangda

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Data Science & ML

Streamlines computational molecular biology tasks including sequence manipulation, NCBI database queries, and structural analysis.

About

Biopython is a comprehensive set of biological computation tools that enables researchers and developers to handle complex bioinformatics workflows. This skill empowers Claude to assist with sequence manipulation, file parsing for FASTA/GenBank/FASTQ formats, and programmatic access to NCBI databases via Entrez. It provides robust patterns for structural biology using Bio.PDB, phylogenetic tree construction, and BLAST result analysis, ensuring your bioinformatics scripts follow industry-standard best practices and efficient data handling techniques.

Key Features

Comprehensive sequence file I/O and format conversion utilities
16 GitHub stars
Programmatic NCBI database access for PubMed and GenBank records
Phylogenetic tree manipulation and visualization capabilities
Pairwise and multiple sequence alignment processing
Structural bioinformatics tools for 3D protein analysis

Use Cases

Automating large-scale DNA/protein sequence translation and statistical analysis
Fetching biological records and publication metadata directly from Entrez APIs
Building and visualizing evolutionary relationships through phylogenetic trees

About

Key Features

Comprehensive sequence file I/O and format conversion utilities
16 GitHub stars
Programmatic NCBI database access for PubMed and GenBank records
Phylogenetic tree manipulation and visualization capabilities
Pairwise and multiple sequence alignment processing
Structural bioinformatics tools for 3D protein analysis

Use Cases

Automating large-scale DNA/protein sequence translation and statistical analysis
Fetching biological records and publication metadata directly from Entrez APIs
Building and visualizing evolutionary relationships through phylogenetic trees