Easy-Prime: a machine learning-based prime editor design tool

Genome Biol. 2021 Aug 19;22(1):235. doi: 10.1186/s13059-021-02458-0.


Prime editing is a revolutionary genome-editing technology that can make a wide range of precise edits in DNA. However, designing highly efficient prime editors (PEs) remains challenging. We develop Easy-Prime, a machine learning-based program trained with multiple published data sources. Easy-Prime captures both known and novel features, such as RNA folding structure, and optimizes feature combinations to improve editing efficiency. We provide optimized PE design for installation of 89.5% of 152,351 GWAS variants. Easy-Prime is available both as a command line tool and an interactive PE design server at: http://easy-prime.cc/ .

Keywords: Machine learning; Prime editor; pegRNA design.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • CRISPR-Cas Systems
  • DNA
  • Gene Editing*
  • HEK293 Cells
  • Humans
  • Machine Learning*
  • RNA, Guide, Kinetoplastida / genetics


  • RNA, Guide
  • DNA