Abstract
Abstract
Background
The Type II clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated proteins (Cas) is a powerful genome editing technology, which is more and more popular in gene function analysis. In CRISPR/Cas, RNA guides Cas nuclease to the target site to perform DNA modification.
Results
The performance of CRISPR/Cas depends on well-designed single guide RNA (sgRNA). However, the off-target effect of sgRNA leads to undesired mutations in genome and limits the use of CRISPR/Cas. Here, we present OffScan, a universal and fast CRISPR off-target detection tool.
Conclusions
OffScan is not limited by the number of mismatches and allows custom protospacer-adjacent motif (PAM), which is the target site by Cas protein. Besides, OffScan adopts the FM-index, which efficiently improves query speed and reduce memory consumption.
Funder
National Key R&D Program of China
Publisher
Springer Science and Business Media LLC
Reference22 articles.
1. Koonin EV, Makarova KS. CRISPR-Cas: an adaptive immunity system in prokaryotes. F1000 Biol Rep. 2009;1:95.
2. Horvath P, Barrangou R. CRISPR/Cas, the immune system of bacteria and archaea. Science. 2010;327(5962):167–70.
3. Memi F, Ntokou A, Papangeli I. CRISPR/Cas9 gene-editing: research technologies, clinical applications and ethical considerations. Semin Perinatol. 2018;S0146-0005(18):30081–8.
4. Lin Y, Cradick TJ, Brown MT, Deshmukh H, Ranjan P, Sarode N, et al. CRISPR/Cas9 systems have off-target activity with insertions or deletions between target DNA and guide RNA sequences. Nucleic Acids Res. 2014;42(11):7473–85.
5. Chen CH, Xiao T, Xu H, Jiang P, Meyer CA, Li W, Brown M, Liu XS. Improved design and analysis of CRISPR knockout screens. Bioinformatics. 2018;34(23):4095–101.
Cited by
14 articles.
订阅此论文施引文献
订阅此论文施引文献，注册后可以免费订阅5篇论文的施引文献，订阅后可以查看论文全部施引文献