Sangsu Bae1,2, Jiyeon Kweon1,2, Heon Seok Kim1,2 & Jin-Soo Kim1,2,*
1Center for Genome Engineering, Institute for Basic Science, Seoul, South Korea.
2Department of Chemistry, Seoul National University, Seoul, South Korea.
*Correspondence to: Jin-Soo Kim
Programmable nucleases such as Cas9 RNA-guided engineered nucleases (RGENs)1 enable gene knockout in cultured cells and organisms by producing site-specific DNA double-strand breaks, whose repair via error-prone nonhomologous end joining gives rise to small insertions and deletions (indels) at target sites, often causing frameshift mutations in a protein-coding sequence2. The efficiency of this method can be reduced by in-frame mutations via microhomology-mediated end joining3, 4 (Fig. 1a). Here we present a computer program that assists in the choice of Cas9 nuclease, zinc-finger nuclease and transcription activator-like effector nuclease (TALEN) target sites, using microhomology prediction to achieve efficient gene disruption in cell lines and whole organisms.