Restriction Mapping

Create Basic Restriction Map

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

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

batch = RestrictionBatch([EcoRI, BamHI, HindIII]) analysis = Analysis(batch, seq)

Print formatted map

analysis.print_as('map')

Output Formats

Map format (visual)

analysis.print_as('map')

Linear format (list)

analysis.print_as('linear')

Tabular format

analysis.print_as('tabulate')

Get as string instead of printing

map_str = analysis.format_as('map') linear_str = analysis.format_as('linear')

Calculate Distances Between Sites

from Bio.Restriction import EcoRI, BamHI

ecori_sites = EcoRI.search(seq) bamhi_sites = BamHI.search(seq)

All cut positions sorted

all_sites = sorted(ecori_sites + bamhi_sites)

Calculate distances between consecutive sites

distances = [] for i in range(len(all_sites) - 1): dist = all_sites[i + 1] - all_sites[i] distances.append((all_sites[i], all_sites[i + 1], dist)) print(f'{all_sites[i]} -> {all_sites[i + 1]}: {dist} bp')

Create Detailed Restriction Map

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

record = SeqIO.read('plasmid.fasta', 'fasta') seq = record.seq seq_len = len(seq)

enzymes = RestrictionBatch([EcoRI, BamHI, HindIII, XhoI, NotI]) analysis = Analysis(enzymes, seq, linear=False)

print(f'Restriction Map: {record.id}') print(f'Length: {seq_len} bp (circular)') print('=' * 50)

results = analysis.full() all_cuts = []

for enzyme, sites in results.items(): for site in sites: all_cuts.append((site, str(enzyme)))

all_cuts.sort(key=lambda x: x[0])

print('\nCut sites (5' -> 3'):') for pos, enz in all_cuts: pct = (pos / seq_len) * 100 print(f' {pos:6d} bp ({pct:5.1f}%) - {enz}')

Text-Based Map Visualization

def draw_restriction_map(seq, results, width=80): '''Draw a simple text restriction map''' seq_len = len(seq) scale = width / seq_len

# Header
print(f'0{" " * (width - 6)}{seq_len}')
print('|' + '-' * (width - 2) + '|')

# Plot each enzyme
for enzyme, sites in results.items():
    if not sites:
        continue
    line = [' '] * width
    for site in sites:
        pos = int(site * scale)
        if pos >= width:
            pos = width - 1
        line[pos] = '|'
    print(''.join(line) + f' {enzyme}')

print('|' + '-' * (width - 2) + '|')

Usage

batch = RestrictionBatch([EcoRI, BamHI, HindIII]) analysis = Analysis(batch, seq) results = analysis.full() draw_restriction_map(seq, results)

Map with GenBank Features

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

record = SeqIO.read('plasmid.gb', 'genbank') seq = record.seq

enzymes = RestrictionBatch([EcoRI, BamHI]) analysis = Analysis(enzymes, seq, linear=False) results = analysis.full()

print('Restriction Sites and Overlapping Features:') print('=' * 60)

for enzyme, sites in results.items(): for site in sites: print(f'\n{enzyme} at position {site}:') for feature in record.features: start = int(feature.location.start) end = int(feature.location.end) if start <= site <= end: feat_type = feature.type label = feature.qualifiers.get('label', feature.qualifiers.get('gene', ['unknown']))[0] print(f' Within {feat_type}: {label} ({start}-{end})')

Export Map to File

def export_restriction_map(seq, results, output_file, seq_name='sequence'): '''Export restriction map to text file''' with open(output_file, 'w') as f: f.write(f'Restriction Map: {seq_name}\n') f.write(f'Length: {len(seq)} bp\n') f.write('=' * 50 + '\n\n')

    all_cuts = []
    for enzyme, sites in results.items():
        for site in sites:
            all_cuts.append((site, str(enzyme)))

    all_cuts.sort()

    f.write('Site\tPosition\tFrom_Start\n')
    for pos, enz in all_cuts:
        f.write(f'{enz}\t{pos}\t{pos}\n')

    f.write('\n\nFragment sizes between sites:\n')
    if all_cuts:
        positions = sorted([c[0] for c in all_cuts])
        for i in range(len(positions) - 1):
            size = positions[i + 1] - positions[i]
            f.write(f'{positions[i]} -> {positions[i + 1]}: {size} bp\n')

Usage

export_restriction_map(seq, results, 'restriction_map.txt', record.id)

Circular Map Coordinates

def circular_distances(sites, seq_len): '''Calculate fragment sizes for circular DNA''' if not sites: return []

sites = sorted(sites)
fragments = []

# Between consecutive sites
for i in range(len(sites) - 1):
    fragments.append(sites[i + 1] - sites[i])

# Wrap-around fragment
wrap = (seq_len - sites[-1]) + sites[0]
fragments.append(wrap)

return fragments

Usage

ecori_sites = EcoRI.search(seq, linear=False) fragments = circular_distances(ecori_sites, len(seq)) print(f'EcoRI fragments (circular): {fragments}')

Related Skills

• restriction-sites - Find where enzymes cut

• enzyme-selection - Choose enzymes for mapping

• fragment-analysis - Analyze fragment sizes