Biopython: Sequence Analysis Toolkit

Biopython: Sequence Analysis Toolkit

Overview

Biopython provides a comprehensive suite of modules for sequence-centric bioinformatics: reading and writing every major biological file format (FASTA, FASTQ, GenBank, GFF), querying NCBI databases programmatically, running BLAST searches and parsing results, aligning sequences pairwise or in multiple-sequence alignments, and building and visualizing phylogenetic trees. This skill focuses on analysis workflows — from NCBI data retrieval through alignment to phylogenetic inference.

For PCR primer design, restriction enzyme digestion, cloning simulation, protein structure analysis (Bio.PDB), and molecular weight/Tm calculations, see biopython-molecular-biology.

When to Use

• Download a gene family from NCBI Nucleotide/Protein, align sequences, and construct a phylogenetic tree
• Parse GenBank or GFF3 annotation files and extract CDS sequences for a set of features
• Run a BLAST search against NCBI nt or nr, filter significant hits, and fetch their full sequences
• Compute pairwise sequence identities or score alignments with BLOSUM62/PAM250 matrices
• Index a large multi-FASTA or FASTQ file with SeqIO.index() for random-access retrieval without loading all sequences into RAM
• Convert between sequence formats (FASTA ↔ GenBank ↔ FASTQ ↔ PHYLIP) in a single call
• Traverse, root, prune, and annotate a Newick or Nexus phylogenetic tree programmatically
• Use pysam instead when working with SAM/BAM/CRAM alignment files and mapped reads
• Use scikit-bio instead when you need ecological diversity metrics (UniFrac, beta diversity) or ordination methods such as PCoA
• Use gget instead for quick gene lookups and one-liner NCBI queries without writing an Entrez pipeline

Prerequisites

• Python packages: biopython, numpy, matplotlib
• Optional tools: MUSCLE or ClustalW installed locally (for Bio.Align.Applications wrappers)
• NCBI access: Set Entrez.email before any E-utilities call; obtain a free API key at https://www.ncbi.nlm.nih.gov/account/ for 10 req/s (default is 3 req/s)
• Local BLAST: BLAST+ installed separately (conda install -c bioconda blast) for offline searches

Check before installing: The tool may already be available in the current environment (e.g., inside a pixi / conda env). Run command -v python first and skip the install commands below if it returns a path. When running inside a pixi project, invoke the tool via pixi run python rather than bare python.

pip install biopython numpy matplotlib
conda install -c bioconda blast  # optional, for local BLAST

Quick Start

from Bio import SeqIO, Entrez
from Bio.SeqUtils import gc_fraction