biopython-molecular-biology
Biopython: Computational Molecular Biology Toolkit
Overview
Biopython is the standard open-source Python library for computational molecular biology, providing modular APIs for sequence handling, biological file parsing, NCBI database access, BLAST searches, protein structure analysis, and phylogenetics. It supports Python 3 and requires NumPy.
When to Use
- Parse and convert biological file formats (FASTA, GenBank, FASTQ, PDB, mmCIF, PHYLIP)
- Fetch sequences or publications from NCBI databases (GenBank, PubMed, Protein) programmatically
- Run and parse BLAST searches (remote NCBI or local BLAST+)
- Perform pairwise or multiple sequence alignments with custom scoring
- Analyze 3D protein structures — distances, angles, DSSP, superimposition
- Build and visualize phylogenetic trees from sequence alignments
- Calculate sequence statistics (GC content, molecular weight, melting temperature)
- Batch-process thousands of sequences with custom filtering logic
- Use
pysaminstead for reading SAM/BAM/CRAM alignment files and working with mapped reads; usescikit-bioinstead for advanced ecological diversity metrics
Prerequisites
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