bio-restriction-sites

Version Compatibility

Reference examples tested with: BioPython 1.83+

Before using code patterns, verify installed versions match. If versions differ:

• Python: pip show <package> then help(module.function) to check signatures

If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying.

Finding Restriction Sites

"Find restriction sites in my DNA sequence" → Locate cut positions for one or more restriction enzymes in linear or circular DNA.

• Python: Bio.Restriction.Analysis(rb, seq, linear=True).full()

Core Pattern

from Bio import SeqIO
from Bio.Restriction import EcoRI, BamHI, HindIII, RestrictionBatch, Analysis

record = SeqIO.read('sequence.fasta', 'fasta')
seq = record.seq

# Single enzyme
sites = EcoRI.search(seq)  # Returns list of cut positions

Search with Single Enzyme

from Bio.Restriction import EcoRI

sites = EcoRI.search(seq)
print(f'EcoRI cuts at positions: {sites}')
print(f'Number of sites: {len(sites)}')

# Check if enzyme cuts
if EcoRI.search(seq):
    print('EcoRI cuts this sequence')
else:
    print('EcoRI does not cut')

Search with Multiple Enzymes

from Bio.Restriction import RestrictionBatch, EcoRI, BamHI, HindIII, XhoI

batch = RestrictionBatch([EcoRI, BamHI, HindIII, XhoI])

# Method 1: batch.search()
results = batch.search(seq)
for enzyme, sites in results.items():
    if sites:
        print(f'{enzyme}: {sites}')

# Method 2: Analysis class
analysis = Analysis(batch, seq)
results = analysis.full()

Use Built-in Enzyme Collections

from Bio.Restriction import AllEnzymes, CommOnly

# All known enzymes (800+)
analysis = Analysis(AllEnzymes, seq)

# Commercially available only
analysis = Analysis(CommOnly, seq)

# Get results
results = analysis.full()
for enzyme, sites in results.items():
    if sites:
        print(f'{enzyme}: {sites}')

Linear vs Circular DNA