Does this skill require a specific version of Biopython?

The skill is optimized for Biopython 1.85 (released January 2025) and requires Python 3 and NumPy to function correctly.

Is it suitable for large-scale genomic data processing?

Yes, Biopython is designed to use iterators for large file parsing, allowing you to process high-throughput sequence data without exhausting system memory.

Which biological file formats are supported?

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

Can I access NCBI databases using this skill?

Yes, it provides streamlined patterns for NCBI's Entrez databases. Note that you must provide an email address and optionally an API key to comply with NCBI rate limits.

Biopython Bioinformatics Toolkit

Name: Biopython Bioinformatics Toolkit
Author: Microck

byMicrock

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108

データサイエンスとML

Simplifies computational molecular biology tasks including sequence analysis, structural bioinformatics, and programmatic NCBI database access.

概要

Biopython provides a comprehensive ecosystem for biological computation, enabling users to perform complex bioinformatics workflows directly within Python. It streamlines the processing of diverse file formats like FASTA and GenBank, facilitates automated searches of NCBI's Entrez databases, and offers robust tools for sequence alignment, structural protein analysis, and phylogenetic tree construction. This skill is essential for researchers and developers needing to automate biological data analysis, manage large-scale genomic datasets, or integrate bioinformatics pipelines into their software projects.

主な機能

Programmatic NCBI Entrez database access for PubMed and GenBank retrieval
Phylogenetic tree manipulation, distance calculation, and visualization
Comprehensive sequence manipulation, translation, and transcription
Structural bioinformatics tools for PDB and mmCIF 3D protein analysis
Automated BLAST search execution and XML result parsing
108 GitHub stars

ユースケース

Analyzing 3D protein structures and calculating molecular distances or RMSD
Automated retrieval and parsing of genomic sequences from NCBI databases
Large-scale sequence alignment and protein motif identification

概要

主な機能

Programmatic NCBI Entrez database access for PubMed and GenBank retrieval
Phylogenetic tree manipulation, distance calculation, and visualization
Comprehensive sequence manipulation, translation, and transcription
Structural bioinformatics tools for PDB and mmCIF 3D protein analysis
Automated BLAST search execution and XML result parsing
108 GitHub stars

ユースケース

Analyzing 3D protein structures and calculating molecular distances or RMSD
Automated retrieval and parsing of genomic sequences from NCBI databases
Large-scale sequence alignment and protein motif identification