biopython skill

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 1.87 (released 30 March 2026). It supports Python 3.10-3.14 and PyPy3.10, and requires NumPy. Biopython 1.87 also addresses CVE-2025-68463 in Bio.Entrez.Parser when parsing untrusted files, so prefer 1.87+ for workflows that parse externally supplied Entrez XML.

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.)
• Performing structural bioinformatics tasks
• Working with population genetics data
• Any other computational molecular biology task

Core Capabilities

Biopython is organized into modular sub-packages, each addressing specific bioinformatics domains:

1. Sequence Handling - Bio.Seq and Bio.SeqIO for sequence manipulation and file I/O
2. Alignment Analysis - Bio.Align and Bio.AlignIO for pairwise and multiple sequence alignments
3. Database Access - Bio.Entrez for programmatic access to NCBI databases
4. BLAST Operations - Bio.Blast for running and parsing BLAST searches
5. Structural Bioinformatics - Bio.PDB for working with 3D protein structures
6. Phylogenetics - Bio.Phylo for phylogenetic tree manipulation and visualization
7. Advanced Features - Motifs, population genetics, sequence utilities, and more

Installation and Setup

Install the current stable Biopython release with an explicit version pin for reproducibility:

uv pip install "biopython==1.87"

For NCBI database access, always set your email address (required by NCBI). For reusable software, set a stable Entrez.tool value and register the tool/email with NCBI. For higher rate limits (10 req/s instead of 3 req/s), read only NCBIAPIKEY from the environment — do not hardcode keys or load unrelated environment variables:

import os
from Bio import Entrez

Entrez.email = "your.email@example.com"  # required — use your real email
Entrez.tool = "your_tool_name"  # optional but recommended for reusable software

# Optional: register at https://www.ncbi.nlm.nih.gov/account/settings/
if api_key := os.environ.get("NCBI_API_KEY"):
    Entrez.api_key = api_key

Using This Skill

This skill provides comprehensive documentation organized by functionality area. When working on a task, consult the relevant reference documentation:

1. Sequence Handling (Bio.Seq & Bio.SeqIO)

Reference: references/sequence_io.md

Use for:

• Creating and manipulating biological sequences
• Reading and writing sequence files (FASTA, GenBank, FASTQ, etc.)
• Converting between file formats
• Extracting sequences from large files
• Sequence translation, transcription, and reverse complement
• Working with SeqRecord objects

Quick example:

from Bio import SeqIO

# Read sequences from FASTA file
for record in SeqIO.parse("sequences.fasta", "fasta"):
    print(f"{record.id}: {len(record.seq)} bp")

# Convert GenBank to FASTA
SeqIO.convert("input.gb", "genbank", "output.fasta", "fasta")

2. Alignment Analysis (Bio.Align & Bio.AlignIO)

Reference: references/alignment.md

Use for:

• Pairwise sequence alignment (global and local)
• Reading and writing multiple sequence alignments
• Using substitution matrices (BLOSUM, PAM)
• Calculating alignment statistics
• Customizing alignment parameters

Quick example:

from Bio import Align

# Pairwise alignment
aligner = Align.PairwiseAligner()
aligner.mode = 'global'
alignments = aligner.align("ACCGGT", "ACGGT")
print(alignments[0])

3. Database Access (Bio.Entrez)

Reference: references/databases.md

Use for:

• Searching NCBI databases (PubMed, GenBank, Protein, Gene, etc.)
• Downloading sequences and records
• Fetching publication information
• Finding related records across databases
• Batch downloading with proper rate limiting

Quick example:

from Bio import Entrez
Entrez.email = "your.email@example.com"

# Search PubMed
handle = Entrez.esearch(db="pubmed", term="biopython", retmax=10)
results = Entrez.read(handle)
handle.close()
print(f"Found {results['Count']} results")

4. BLAST Operations (Bio.Blast)

Reference: references/blast.md

Use for:

• Running BLAST searches via NCBI web services
• Running local BLAST searches
• Parsing BLAST XML output
• Filtering results by E-value or identity
• Extracting hit sequences

Quick example:

from Bio.Blast import NCBIWWW, NCBIXML

# Run BLAST search
result_handle = NCBIWWW.qblast("blastn", "nt", "ATCGATCGATCG")
blast_record = NCBIXML.read(result_handle)

# Display top hits
for alignment in blast_record.alignments[:5]:
    print(f"{alignment.title}: E-value={alignment.hsps[0].expect}")

5. Structural Bioinformatics (Bio.PDB)

Reference: references/structure.md

Use for:

• Parsing PDB and mmCIF structure files
• Navigating protein structure hierarchy (SMCRA: Structure/Model/Chain/Residue/Atom)
• Calculating distances, angles, and dihedrals
• Secondary structure assignment (DSSP)
• Structure superimposition and RMSD calculation
• Extracting sequences from structures

Quick example:

from Bio.PDB import PDBParser

# Parse structure
parser = PDBParser(QUIET=True)
structure = parser.get_structure("1crn", "1crn.pdb")

# Calculate distance between alpha carbons
chain = structure[0]["A"]
distance = chain[10]["CA"] - chain[20]["CA"]
print(f"Distance: {distance:.2f} Å")

6. Phylogenetics (Bio.Phylo)

Reference: references/phylogenetics.md

Use for:

• Reading and writing phylogenetic trees (Newick, NEXUS, phyloXML)
• Building trees from distance matrices or alignments
• Tree manipulation (pruning, rerooting, ladderizing)
• Calculating phylogenetic distances
• Creating consensus trees
• Visualizing trees

Quick example:

from Bio import Phylo

# Read and visualize tree
tree = Phylo.read("tree.nwk", "newick")
Phylo.draw_ascii(tree)

# Calculate distance
distance = tree.distance("Species_A", "Species_B")
print(f"Distance: {distance:.3f}")

7. Advanced Features

Reference: references/advanced.md

Use for:

• Sequence motifs (Bio.motifs) - Finding and analyzing motif patterns
• Population genetics (Bio.PopGen) - GenePop files, Fst calculations, Hardy-Weinberg tests
• Sequence utilities (Bio.SeqUtils) - GC content, melting temperature, molecular weight, protein analysis
• Restriction analysis (Bio.Restriction) - Finding restriction enzyme sites
• Clustering (Bio.Cluster) - K-means and hierarchical clustering
• Genome diagrams (GenomeDiagram) - Visualizing genomic features

Quick example:

from Bio.SeqUtils import gc_fraction, molecular_weight
from Bio.Seq import Seq

seq = Seq("ATCGATCGATCG")
print(f"GC content: {gc_fraction(seq):.2%}")
print(f"Molecular weight: {molecular_weight(seq, seq_type='DNA'):.2f} g/mol")

General Workflow Guidelines

Reading Documentation