bio-restriction-enzyme-selection

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.

Enzyme Selection

"Find enzymes that cut my sequence once" → Search restriction enzyme databases by cut frequency, overhang type, commercial availability, or compatible ends for cloning.

• Python: Bio.Restriction.Analysis(rb, seq) with RestrictionBatch filters

Find Enzymes by Cut Frequency

from Bio import SeqIO
from Bio.Restriction import Analysis, CommOnly, AllEnzymes

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

analysis = Analysis(CommOnly, seq)

# Enzymes that cut exactly once (good for linearization)
once_cutters = analysis.once_cutters()

# Enzymes that cut exactly twice (good for excision)
twice_cutters = analysis.twice_cutters()

# Enzymes that don't cut (good for cloning insert)
non_cutters = analysis.only_dont_cut()

# All enzymes that cut (any number of times)
all_cutters = analysis.only_cut()

Find Non-Cutters for Insert

from Bio.Restriction import Analysis, CommOnly

# Find enzymes that don't cut your insert
insert_seq = record.seq
analysis = Analysis(CommOnly, insert_seq)

non_cutters = analysis.only_dont_cut()
print('Enzymes that do not cut the insert:')
for enzyme in non_cutters:
    print(f'  {enzyme}')

Find Compatible Enzyme Pairs

from Bio.Restriction import EcoRI, BamHI, BglII, XhoI, SalI

# Check if enzymes produce compatible overhangs
def find_compatible_enzymes(enzyme):
    '''Find enzymes with same overhang'''
    compatible = enzyme.compatible_end()
    print(f'{enzyme} is compatible with: {compatible}')

find_compatible_enzymes(BamHI)  # Compatible with BglII
find_compatible_enzymes(XhoI)   # Compatible with SalI