Finding Restriction Sites

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

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

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

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

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

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

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=False for 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