Biopython: Computational Molecular Biology Toolkit

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 pysam instead for reading SAM/BAM/CRAM alignment files and working with mapped reads; use scikit-bio instead for advanced ecological diversity metrics

Prerequisites

• Python packages: biopython, numpy, matplotlib (for tree visualization)
• Data requirements: Sequence files (FASTA, GenBank, FASTQ) or accession IDs for NCBI access
• Environment: Python 3.8+; NCBI Entrez requires email registration

pip install biopython numpy matplotlib

Quick Start

from Bio import SeqIO
from Bio.Seq import Seq
from Bio.SeqUtils import gc_fraction

# Parse a FASTA file and compute basic statistics
records = list(SeqIO.parse("sequences.fasta", "fasta"))
print(f"Sequences loaded: {len(records)}")

seq = records[0].seq