bio-genome-engineering-base-editing-design

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.

Base Editing Design

"Design a base editor guide for my C-to-T conversion" → Identify guide sequences that position the target nucleotide within the editing window of cytosine (CBE) or adenine (ABE) base editors, predicting editing outcomes and bystander effects.

• Python: editing window analysis with Bio.Seq, BE-Hive outcome prediction

Base Editor Types

Cytosine Base Editors (CBE):
- Convert C to T (or G to A on opposite strand)
- Examples: BE3, BE4, BE4max, AncBE4max
- Editing window: Positions 4-8 (PAM-distal numbering)

Adenine Base Editors (ABE):
- Convert A to G (or T to C on opposite strand)
- Examples: ABE7.10, ABE8e, ABE8.20
- Editing window: Positions 4-7 (narrower than CBE)

Position numbering:
Position 1 = PAM-proximal (next to NGG)
Position 20 = PAM-distal (5' end of spacer)
Editing window is typically positions 4-8 from PAM-distal end

Find Editable Positions

Goal: Identify guide sequences that place a target nucleotide within the base editor's editing window while minimizing bystander edits.

Approach: Scan for PAM sites in both orientations, calculate where the target base falls within the spacer, filter guides where the target lands in the CBE (positions 4-8) or ABE (positions 4-7) editing window, and rank by fewest bystander bases in the window.

from Bio.Seq import Seq
import re

# Editing window positions (1-indexed from PAM-distal end)
# Position 1 is first nt of spacer, position 20 is adjacent to PAM
CBE_WINDOW = (4, 8)   # BE4max optimal window
ABE_WINDOW = (4, 7)   # ABE8e optimal window

def find_cbe_targets(sequence, target_c_position):
    '''Find guides that place a C in the CBE editing window

    Args:
        sequence: DNA sequence containing the target C
        target_c_position: 0-indexed position of C to edit

    Returns:
        List of guide options with editing predictions
    '''
    sequence = sequence.upper()
    guides = []

    # Search for PAMs that would place target C in window
    for pam_match in re.finditer(r'(?=(.GG))', sequence):
        pam_pos = pam_match.start()

        # Calculate where target C falls in the spacer
        spacer_start = pam_pos - 20
        if spacer_start < 0:
            continue

        c_position_in_spacer = target_c_position - spacer_start + 1  # 1-indexed

        # Check if C is in editing window
        if CBE_WINDOW[0] <= c_position_in_spacer <= CBE_WINDOW[1]:
            spacer = sequence[spacer_start:pam_pos]

            # Find bystander Cs in window (may also be edited)
            bystanders = []
            for i in range(CBE_WINDOW[0] - 1, CBE_WINDOW[1]):
                if i < len(spacer) and spacer[i] == 'C' and (spacer_start + i) != target_c_position:
                    bystanders.append(i + 1)

            guides.append({
                'spacer': spacer,
                'pam_position': pam_pos,
                'target_position_in_spacer': c_position_in_spacer,
                'bystander_cs': bystanders,
                'bystander_count': len(bystanders),
                'strand': '+'
            })

    # Sort by fewest bystanders
    return sorted(guides, key=lambda x: x['bystander_count'])


def find_abe_targets(sequence, target_a_position):
    '''Find guides that place an A in the ABE editing window'''
    sequence = sequence.upper()
    guides = []

    for pam_match in re.finditer(r'(?=(.GG))', sequence):
        pam_pos = pam_match.start()
        spacer_start = pam_pos - 20
        if spacer_start < 0:
            continue

        a_position_in_spacer = target_a_position - spacer_start + 1

        if ABE_WINDOW[0] <= a_position_in_spacer <= ABE_WINDOW[1]:
            spacer = sequence[spacer_start:pam_pos]

            bystanders = []
            for i in range(ABE_WINDOW[0] - 1, ABE_WINDOW[1]):
                if i < len(spacer) and spacer[i] == 'A' and (spacer_start + i) != target_a_position:
                    bystanders.append(i + 1)

            guides.append({
                'spacer': spacer,
                'pam_position': pam_pos,
                'target_position_in_spacer': a_position_in_spacer,
                'bystander_as': bystanders,
                'bystander_count': len(bystanders),
                'strand': '+'
            })

    return sorted(guides, key=lambda x: x['bystander_count'])