biopython
Biopython: Computational Molecular Biology in Python
Overview
Biopython is a comprehensive set of freely available Python tools for biological computation. It provides functionality for sequence manipulation, file I/O, database access, structural bioinformatics, phylogenetics, and many other bioinformatics tasks. The current version is Biopython 1.85 (released January 2025), which supports Python 3 and requires NumPy.
When to Use This Skill
Use this skill when:
- Working with biological sequences (DNA, RNA, or protein)
- Reading, writing, or converting biological file formats (FASTA, GenBank, FASTQ, PDB, mmCIF, etc.)
- Accessing NCBI databases (GenBank, PubMed, Protein, Gene, etc.) via Entrez
- Running BLAST searches or parsing BLAST results
- Performing sequence alignments (pairwise or multiple sequence alignments)
- Analyzing protein structures from PDB files
- Creating, manipulating, or visualizing phylogenetic trees
- Finding sequence motifs or analyzing motif patterns
- Calculating sequence statistics (GC content, molecular weight, melting temperature, etc.)
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