design-base-editor-sgrnas

name	design-base-editor-sgrnas
description	Design base editor sgRNAs for a given gene. Fetches exonic sequence from Ensembl, scans for all NGG (or NG/NGA) PAM sites, filters for guides where a cytosine (CBE) or adenine (ABE) falls in the editing window, scores guides for efficiency and bystander risk, and returns a ranked table. Supports CBE (C→T), ABE (A→G), and dual-base editors for human, mouse, and monkey.

Base Editor sgRNA Design

Purpose

Design sgRNAs for base editing experiments. Given a gene symbol, fetch its coding exon sequences from Ensembl, identify all valid protospacers with a target base (C for CBE, A for ABE) in the editing window, score each guide, and return a ranked table with full annotation of editing outcomes.

Use when

• the user wants to design base editor sgRNAs for a gene
• the user mentions CBE, ABE, cytosine base editor, adenine base editor, base editing
• the user wants to introduce a specific point mutation (e.g., "install a stop codon", "correct a missense variant")
• the user wants to model a disease mutation via base editing
• the user asks about BE3, BE4max, ABE7.10, ABE8e, AncBE4max, or similar editors
• the user wants guides that avoid bystander edits

Do not use when

• the user wants standard CRISPR KO guides (use design-sgrnas-by-gene)
• the user wants prime editor pegRNA design (different mechanism)
• the user wants guides for a non-coding region without specifying coordinates
• the user wants CRISPRi or CRISPRa (dCas9-based, no editing window)

Supported editors and their properties

Editor	Type	Edit	PAM	Window (protospacer positions)
BE3	CBE	C→T	NGG	4–8
BE4max / AncBE4max	CBE	C→T	NGG	4–8
ABE7.10	ABE	A→G	NGG	4–7
ABE8e	ABE	A→G	NGG	4–8
ABE8.20m	ABE	A→G	NGG	4–8
NG-CBE	CBE	C→T	NG	4–8
NG-ABE	ABE	A→G	NG	4–8
SpRY-CBE	CBE	C→T	NRN/NYN	4–8
SpRY-ABE	ABE	A→G	NRN/NYN	4–8
dual	CBE+ABE	C→T and A→G	NGG	4–8

Positions are counted from the PAM-distal end (position 1 = most 5′ of protospacer).

Inputs

• --gene — gene symbol (e.g., TP53, KRAS, BRCA1). Required.
• --organism — human (default), mouse, or monkey
• --editor — editor name or type: CBE, ABE, dual, BE3, BE4max, ABE7.10, ABE8e, NG-CBE, NG-ABE, SpRY-CBE, SpRY-ABE (default: CBE)
• --window-start — editing window start position (default: editor-specific)
• --window-end — editing window end position (default: editor-specific)
• --pam — PAM sequence: NGG (default), NG, or NRN
• --region — sequence scope: cds (coding sequence only, default), exon (all exons), transcript
• --allow-bystander — include guides with bystander C/A in window (default: False)
• --max-bystander — max allowed bystander editable bases (default: 0; use 1-2 if --allow-bystander)
• --top-n — number of top guides to return (default: 20)
• --transcript-id — restrict to a specific Ensembl transcript ID
• --target-aa-pos — target a specific amino acid position (e.g., 12 for KRAS G12)
• --outdir — output directory (default: ./base_editor_results/)
• --prefix — output file prefix (default: gene symbol)

Outputs

File	Description
{prefix}_base_editor_guides.tsv	Full ranked guide table
{prefix}_top_guides.tsv	Top N guides (filtered, scored)
{prefix}_editing_summary.png	Editing window heatmap across protospacer
{prefix}_guide_map.png	Guide positions mapped onto gene exon structure
{prefix}_bystander_report.tsv	Bystander edit analysis per guide

Guide table columns

Column	Description
rank	Final rank (1 = best)
sgrna_seq	20 nt protospacer sequence (5′→3′)
pam	PAM sequence
strand	+ or -
chrom	Chromosome
start / end	Genomic coordinates of protospacer
exon_id	Ensembl exon ID
target_base	Target base (C or A)
window_positions	Positions of editable bases in window
edit_outcomes	Predicted amino acid changes
bystander_count	Number of bystander editable bases in window
gc_content	GC% of protospacer
efficiency_score	Predicted on-target efficiency (0–1)
bystander_penalty	Penalty for co-editing risk (lower = cleaner)
final_score	Composite ranking score

Execution

# Basic CBE guide design for TP53
python scripts/design_base_editor_sgrnas.py \
  --gene TP53 \
  --editor CBE \
  --outdir results/

# ABE8e guides for KRAS, targeting codon 12
python scripts/design_base_editor_sgrnas.py \
  --gene KRAS \
  --editor ABE8e \
  --target-aa-pos 12 \
  --outdir results/

# Dual-base editor, no bystander edits allowed
python scripts/design_base_editor_sgrnas.py \
  --gene EGFR \
  --editor dual \
  --allow-bystander \
  --max-bystander 1 \
  --outdir results/

# Mouse gene, NG-CBE with relaxed PAM
python scripts/design_base_editor_sgrnas.py \
  --gene Trp53 \
  --organism mouse \
  --editor NG-CBE \
  --pam NG \
  --outdir results/

Parameter decision guide

Signal in user request	Parameter to set
"CBE", "cytosine base editor", "C to T", "C→T"	--editor CBE
"ABE", "adenine base editor", "A to G", "A→G"	--editor ABE
"BE3"	--editor BE3 (window 4–8, NGG PAM)
"BE4max", "AncBE4max"	--editor BE4max (window 4–8, NGG PAM)
"ABE7.10"	--editor ABE7.10 (window 4–7)
"ABE8e", "ABE8"	--editor ABE8e (window 4–8)
"NG PAM", "NG editor", "more targets"	--editor NG-CBE or --editor NG-ABE with --pam NG
"SpRY", "PAM-flexible"	--editor SpRY-CBE or --editor SpRY-ABE with --pam NRN
"both CBE and ABE", "dual base editor"	--editor dual
"clean edit", "no bystander", "single edit"	--allow-bystander NOT set (default off)
"allow some bystander", "1 bystander ok"	--allow-bystander --max-bystander 1
"codon 12", "position 12", "G12D"	--target-aa-pos 12
"coding sequence only", "CDS"	--region cds (default)
"all exons"	--region exon
"mouse", "Mus musculus"	--organism mouse
"monkey", "cynomolgus"	--organism monkey
"top 10", "best 10"	--top-n 10
"specific transcript"	--transcript-id ENST...