Prime Editing Design Tool

This website designs pegRNAs and secondary sgRNAs for PE2, PE3 and PE3b prime editors for ClinVar human pathogenic variants.

Quick start guide:

  1. 1) Click on the Prime editing designer tab above.
  2. 2) Enter a gene symbol or ClinVar ID. The tool will design and score pegRNAs and
    PE3/3b sgRNAs for browsing and download.

Sanjana Lab

Sanjana Lab

Designing Custom Prime Editors

To design prime editors of your own, please refer to our Git archive which contains both an installation guide and a tutorial for custom prime editor design.

The custom R scripts may be adapted for the design of prime editors for any species as shown in our tutorial (using an example for prime editing design in zebrafish). After generation of pegRNAs and sgRNAs with the R scripts, we evaluate on-target/off-target scores (and intersections with common dbSNP variants, if relevant) using the scripts listed under the Flashfry analysis and intersection analysis directories respectively.

Sanjana Lab

Thank you for using the Prime Editing Design web-tool.

All source code for our work is available on our Git archive. We also welcome feedback or questions: Email us at

Related resources:

  • Anzalone et al. Search-and-replace genome editing without double-strand breaks or donor DNA. Nature (2019).
  • Legut, Daniloski et al. High-Throughput Screens of PAM-Flexible Cas9 Variants for Gene Knockout Cell Reports (2020).

  • For those interested in designing other types of CRISPR reagents for stand-alone use or multiplexed approaches in conjunction with prime editing, please see some of our other online tools:

  • Cas13design

  • Sanjana Lab