Cas-OFFinder：一种快速、通用的算法，用于搜索 Cas9 RNA 引导的内切酶的潜在脱靶位点。
Cas-OFFinder: a fast and versatile algorithm that searches for potential off-target sites of Cas9 RNA-guided endonucleases.
机构信息
National Creative Research Initiatives Center for Genome Engineering, Department of Chemistry and Department of Physics and Astronomy, Seoul National University, 599 Gwanak-ro, Seoul 151-742, South Korea.
出版信息
Bioinformatics. 2014 May 15;30(10):1473-5. doi: 10.1093/bioinformatics/btu048. Epub 2014 Jan 24.
SUMMARY
The Type II clustered regularly interspaced short palindromic repeats (CRISPR)/Cas system is an adaptive immune response in prokaryotes, protecting host cells against invading phages or plasmids by cleaving these foreign DNA species in a targeted manner. CRISPR/Cas-derived RNA-guided engineered nucleases (RGENs) enable genome editing in cultured cells, animals and plants, but are limited by off-target mutations. Here, we present a novel algorithm termed Cas-OFFinder that searches for potential off-target sites in a given genome or user-defined sequences. Unlike other algorithms currently available for identification of RGEN off-target sites, Cas-OFFinder is not limited by the number of mismatches and allows variations in protospacer-adjacent motif sequences recognized by Cas9, the essential protein component in RGENs. Cas-OFFinder is available as a command-line program or accessible via our website.
AVAILABILITY AND IMPLEMENTATION
Cas-OFFinder free access at http://www.rgenome.net/cas-offinder.
CONTACT
摘要
II 型簇状规律间隔短回文重复序列 (CRISPR)/Cas 系统是原核生物的一种适应性免疫反应，通过靶向切割这些外来 DNA 物种来保护宿主细胞免受入侵噬菌体或质粒的侵害。基于 CRISPR/Cas 的 RNA 指导工程化核酸酶 (RGEN) 可实现在培养细胞、动物和植物中的基因组编辑，但受到脱靶突变的限制。在这里，我们提出了一种称为 Cas-OFFinder 的新算法，可在给定基因组或用户定义的序列中搜索潜在的脱靶位点。与目前可用于识别 RGEN 脱靶位点的其他算法不同，Cas-OFFinder 不受错配数量的限制，并允许 Cas9（RGEN 中必不可少的蛋白成分）识别的原间隔区相邻基序序列发生变化。Cas-OFFinder 可作为命令行程序使用，也可通过我们的网站访问。
可用性和实现
Cas-OFFinder 可在 http://www.rgenome.net/cas-offinder 免费使用。
联系方式
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