biopython

Biopython - Bioinformatics Library

Industry-standard Python library for computational biology and bioinformatics workflows.

When to Use

• Parsing and manipulating biological sequences (DNA, RNA, protein)
• Reading and writing sequence files (FASTA, FASTQ, GenBank, EMBL, SwissProt)
• Performing sequence alignments (pairwise and multiple)
• Running and parsing BLAST searches
• Analyzing protein structures from PDB files
• Calculating sequence statistics and molecular weights
• Translating DNA to protein sequences
• Finding restriction enzyme sites
• Building and analyzing phylogenetic trees
• Accessing NCBI databases (Entrez, PubMed)
• Computing sequence motifs and patterns
• Analyzing next-generation sequencing data

Reference Documentation

Official docs: https://biopython.org/
Tutorial: https://biopython.org/DIST/docs/tutorial/Tutorial.html
Search patterns: SeqIO.parse, Seq, AlignIO, NCBIWWW.qblast, PDBParser

Core Principles

Use Biopython For

Task	Module	Example
Create sequences	Seq	Seq("ATCG")
Read sequence files	SeqIO	SeqIO.parse("file.fasta", "fasta")
Pairwise alignment	pairwise2	pairwise2.align.globalxx(s1, s2)
Multiple alignment	AlignIO	AlignIO.read("align.fasta", "fasta")
BLAST searches	NCBIWWW	NCBIWWW.qblast("blastn", "nr", seq)
PDB structures	PDB.PDBParser	PDBParser().get_structure()
Phylogenetic trees	Phylo	Phylo.read("tree.xml", "phyloxml")
NCBI databases	Entrez	Entrez.esearch(db="nucleotide")

Do NOT Use For

• High-performance genome assembly (use SPAdes, Canu)
• Variant calling from BAM files (use GATK, BCFtools)
• RNA-seq differential expression (use DESeq2, edgeR)
• Protein structure prediction (use AlphaFold, RoseTTAFold)
• Large-scale metagenomics (use specialized pipelines)

Quick Reference

Installation

# pip (recommended)
pip install biopython

# With optional dependencies
pip install biopython[extra]

# conda
conda install -c conda-forge biopython

# Development version
pip install git+https://github.com/biopython/biopython.git