biopython

SKILL.md

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 1.85 (released January 2025), which supports Python 3 and requires NumPy.

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:

Sequence Handling - Bio.Seq and Bio.SeqIO for sequence manipulation and file I/O

Alignment Analysis - Bio.Align and Bio.AlignIO for pairwise and multiple sequence alignments

Database Access - Bio.Entrez for programmatic access to NCBI databases

BLAST Operations - Bio.Blast for running and parsing BLAST searches

Structural Bioinformatics - Bio.PDB for working with 3D protein structures

Phylogenetics - Bio.Phylo for phylogenetic tree manipulation and visualization

Advanced Features - Motifs, population genetics, sequence utilities, and more

Installation and Setup

Install Biopython using pip (requires Python 3 and NumPy):

uv pip install biopython

For NCBI database access, always set your email address (required by NCBI):

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

# Optional: API key for higher rate limits (10 req/s instead of 3 req/s)
Entrez.api_key = "your_api_key_here"

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

When a user asks about a specific Biopython task:

Identify the relevant module based on the task description

Read the appropriate reference file using the Read tool

Extract relevant code patterns and adapt them to the user's specific needs

Combine multiple modules when the task requires it

Example search patterns for reference files:

# Find information about specific functions
grep -n "SeqIO.parse" references/sequence_io.md

# Find examples of specific tasks
grep -n "BLAST" references/blast.md

# Find information about specific concepts
grep -n "alignment" references/alignment.md

Writing Biopython Code

Follow these principles when writing Biopython code:

Import modules explicitly

from Bio import SeqIO, Entrez
from Bio.Seq import Seq

Set Entrez email when using NCBI databases

Entrez.email = "your.email@example.com"

Use appropriate file formats - Check which format best suits the task

# Common formats: "fasta", "genbank", "fastq", "clustal", "phylip"

Handle files properly - Close handles after use or use context managers

with open("file.fasta") as handle:
    records = SeqIO.parse(handle, "fasta")

Use iterators for large files - Avoid loading everything into memory

for record in SeqIO.parse("large_file.fasta", "fasta"):
    # Process one record at a time

Handle errors gracefully - Network operations and file parsing can fail

try:
    handle = Entrez.efetch(db="nucleotide", id=accession)
except HTTPError as e:
    print(f"Error: {e}")

Common Patterns

Pattern 1: Fetch Sequence from GenBank

from Bio import Entrez, SeqIO

Entrez.email = "your.email@example.com"

# Fetch sequence
handle = Entrez.efetch(db="nucleotide", id="EU490707", rettype="gb", retmode="text")
record = SeqIO.read(handle, "genbank")
handle.close()

print(f"Description: {record.description}")
print(f"Sequence length: {len(record.seq)}")

Pattern 2: Sequence Analysis Pipeline

from Bio import SeqIO
from Bio.SeqUtils import gc_fraction

for record in SeqIO.parse("sequences.fasta", "fasta"):
    # Calculate statistics
    gc = gc_fraction(record.seq)
    length = len(record.seq)

    # Find ORFs, translate, etc.
    protein = record.seq.translate()

    print(f"{record.id}: {length} bp, GC={gc:.2%}")

Pattern 3: BLAST and Fetch Top Hits

from Bio.Blast import NCBIWWW, NCBIXML
from Bio import Entrez, SeqIO

Entrez.email = "your.email@example.com"

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

# Get top hit accessions
accessions = [aln.accession for aln in blast_record.alignments[:5]]

# Fetch sequences
for acc in accessions:
    handle = Entrez.efetch(db="nucleotide", id=acc, rettype="fasta", retmode="text")
    record = SeqIO.read(handle, "fasta")
    handle.close()
    print(f">{record.description}")

Pattern 4: Build Phylogenetic Tree from Sequences

from Bio import AlignIO, Phylo
from Bio.Phylo.TreeConstruction import DistanceCalculator, DistanceTreeConstructor

# Read alignment
alignment = AlignIO.read("alignment.fasta", "fasta")

# Calculate distances
calculator = DistanceCalculator("identity")
dm = calculator.get_distance(alignment)

# Build tree
constructor = DistanceTreeConstructor()
tree = constructor.nj(dm)

# Visualize
Phylo.draw_ascii(tree)

Best Practices

Always read relevant reference documentation before writing code

Use grep to search reference files for specific functions or examples

Validate file formats before parsing

Handle missing data gracefully - Not all records have all fields

Cache downloaded data - Don't repeatedly download the same sequences

Respect NCBI rate limits - Use API keys and proper delays

Test with small datasets before processing large files

Keep Biopython updated to get latest features and bug fixes

Use appropriate genetic code tables for translation

Document analysis parameters for reproducibility

Troubleshooting Common Issues

Issue: "No handlers could be found for logger 'Bio.Entrez'"

Solution: This is just a warning. Set Entrez.email to suppress it.

Issue: "HTTP Error 400" from NCBI

Solution: Check that IDs/accessions are valid and properly formatted.

Issue: "ValueError: EOF" when parsing files

Solution: Verify file format matches the specified format string.

Issue: Alignment fails with "sequences are not the same length"

Solution: Ensure sequences are aligned before using AlignIO or MultipleSeqAlignment.

Issue: BLAST searches are slow

Solution: Use local BLAST for large-scale searches, or cache results.

Issue: PDB parser warnings

Solution: Use PDBParser(QUIET=True) to suppress warnings, or investigate structure quality.

Additional Resources

Official Documentation: https://biopython.org/docs/latest/

Tutorial: https://biopython.org/docs/latest/Tutorial/

Cookbook: https://biopython.org/docs/latest/Tutorial/ (advanced examples)

GitHub: https://github.com/biopython/biopython

Mailing List: biopython@biopython.org

Quick Reference

To locate information in reference files, use these search patterns:

# Search for specific functions
grep -n "function_name" references/*.md

# Find examples of specific tasks
grep -n "example" references/sequence_io.md

# Find all occurrences of a module
grep -n "Bio.Seq" references/*.md

Summary

Biopython provides comprehensive tools for computational molecular biology. When using this skill:

Identify the task domain (sequences, alignments, databases, BLAST, structures, phylogenetics, or advanced)

Consult the appropriate reference file in the references/ directory

Adapt code examples to the specific use case

Combine multiple modules when needed for complex workflows

Follow best practices for file handling, error checking, and data management

The modular reference documentation ensures detailed, searchable information for every major Biopython capability.
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