Finding Restriction Sites
Core Pattern
python
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
python
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
python
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
python
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
python
from Bio.Restriction import EcoRI, Analysis, RestrictionBatch # Linear DNA (default) sites_linear = EcoRI.search(seq, linear=True) # Circular DNA (plasmid) sites_circular = EcoRI.search(seq, linear=False) # With Analysis class batch = RestrictionBatch([EcoRI, BamHI]) analysis = Analysis(batch, seq, linear=False) # Circular
Filter Results
python
from Bio.Restriction import Analysis, CommOnly analysis = Analysis(CommOnly, seq) # Only enzymes that cut analysis.print_that_cut() # Only enzymes that don't cut (non-cutters) analysis.print_that_dont_cut() # Enzymes that cut once analysis.print_once_cutters() # Enzymes that cut twice analysis.print_twice_cutters() # Get as dictionary cutters = analysis.only_cut() non_cutters = analysis.only_dont_cut() once_cutters = analysis.once_cutters() twice_cutters = analysis.twice_cutters()
Get Enzyme Information
python
from Bio.Restriction import EcoRI
# Recognition sequence
print(f'Site: {EcoRI.site}') # GAATTC
print(f'Esite: {EcoRI.esite}') # Recognition with cut position
# Cut characteristics
print(f'Overhang: {EcoRI.ovhg}') # 4 (positive = 5' overhang)
print(f'Blunt: {EcoRI.is_blunt()}') # False
print(f'5\' overhang: {EcoRI.is_5overhang()}') # True
print(f'3\' overhang: {EcoRI.is_3overhang()}') # False
# Overhang sequence
print(f'Overhang seq: {EcoRI.ovhgseq}') # AATT
# Isoschizomers (same recognition, different cut)
print(f'Isoschizomers: {EcoRI.isoschizomers()}')
# Compatible enzymes (same overhang)
print(f'Compatible: {EcoRI.compatible_end()}')
Common Cloning Enzymes
python
from Bio.Restriction import (
EcoRI, BamHI, HindIII, XhoI, SalI, NotI, XbaI, SpeI,
NcoI, NdeI, BglII, PstI, KpnI, SacI, EcoRV, SmaI
)
common_enzymes = RestrictionBatch([
EcoRI, BamHI, HindIII, XhoI, SalI, NotI, XbaI,
NcoI, NdeI, BglII, PstI, KpnI, SacI, EcoRV, SmaI
])
analysis = Analysis(common_enzymes, seq)
results = analysis.full()
Access Enzymes by Name
python
from Bio.Restriction import AllEnzymes
# Get enzyme by string name
ecori = AllEnzymes.get('EcoRI')
sites = ecori.search(seq)
# Check if enzyme exists
if 'EcoRI' in AllEnzymes:
print('EcoRI is in database')
Search Multiple Sequences
python
from Bio import SeqIO
from Bio.Restriction import RestrictionBatch, EcoRI, BamHI
batch = RestrictionBatch([EcoRI, BamHI])
for record in SeqIO.parse('sequences.fasta', 'fasta'):
analysis = Analysis(batch, record.seq)
results = analysis.full()
print(f'{record.id}:')
for enzyme, sites in results.items():
if sites:
print(f' {enzyme}: {sites}')
Notes
- •Positions are 1-based - first base is position 1
- •Cut position - where enzyme cuts (between bases)
- •Linear default - set
linear=Falsefor circular DNA - •Case insensitive - recognition matches regardless of case
- •Ambiguous bases - some enzymes recognize N, R, Y, etc.
Related Skills
- •restriction-mapping - Visualize cut positions on sequence
- •enzyme-selection - Choose enzymes by criteria
- •fragment-analysis - Analyze resulting fragments