Base Editing Designer — CBE / ABE gRNA & Bystander/Codon Report
Find CBE (C→T) or ABE (A→G) base-editing gRNAs that place your target base in the editor's activity window, with bystander flags and amino-acid consequences.
🌐 Runs on the SeqBench API — also callable via REST & MCP, and in bulk from the batch tools
Pick a base editor (CBE for C→T, ABE for A→G) and paste a target, and get every SpCas9 gRNA whose activity window (the PAM-distal positions where the deaminase acts) places an editable base. Each guide lists the base(s) it would edit, flags bystander edits (more than one editable base in the same window — the main specificity concern in base editing), and, when you supply a CDS reading frame, classifies each edit's amino-acid consequence as silent, missense, nonsense, or stop-loss. Guides with exactly one editable base (bystander-free) are ranked first. Both strands are handled correctly: a C→T on the protospacer of a reverse-strand guide is reported as the forward-strand G→A it actually is.
How to use the Base Editing Designer tool
- 1Choose a base editor and paste the target region (optionally give the 1-based CDS frame start to see amino-acid effects).
- 2Review the ranked guides — bystander-free first — each showing the edited position(s), the forward-strand base change, and the codon consequence.
- 3Pick a guide whose window cleanly captures your intended base with the fewest bystanders, and copy the spacer.
Frequently asked questions
Which base editors are included?
Cytosine base editors BE3 and BE4max (C→T) and adenine base editors ABE7.10 and ABE8e (A→G), each with its widely-cited activity window on the 20-nt protospacer (PAM-distal position 1). ABE8e uses a wider window than ABE7.10, reflecting its broader editing range.
What is a bystander edit and why does it matter?
Base editors edit every occurrence of the target base (all Cs for a CBE, all As for an ABE) within their activity window, not just the one you want. Extra edits are "bystanders" and are the main source of unintended changes. This tool counts them per guide and ranks bystander-free guides (exactly one editable base in the window) first.
How is the amino-acid consequence computed?
When you give a 1-based CDS reading-frame start, each edited forward-strand base is mapped to its codon and the resulting codon is translated, classifying the change as silent, missense, nonsense (introduces a stop), or stop-loss. Without a frame, edits are reported at the nucleotide level only.
Does it check off-target activity or predict editing efficiency?
No. It places edits by the editor's canonical activity window and reports consequences deterministically; it does not model per-guide editing efficiency or genome-wide off-targets (no reference genome in-browser). Validate the spacer's specificity separately.
Is my sequence uploaded, and can I use this from code?
The scan runs on SeqBench's stateless API (the same pure function) and nothing is stored. The base_editing_design tool is available via the REST API and MCP server.
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