GPTomics/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

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