CasOT: a genome-wide Cas9/gRNA off-target searching tool

By An Xiao, Zhenchao Cheng, Lei Kong, Zuoyan Zhu, Shuo Lin, Ge Gao. Bioinform., 2014

351 citations recorded by the source corpus.

The CRISPR/Cas or Cas9/guide RNA system is a newly developed, easily engineered and highly effective tool for gene targeting; it has considerable off-target effects in cultured human cells and in several organisms. However, the Cas9/guide RNA target site is too short for existing alignment tools to exhaustively and effectively identify potential off-target sites. CasOT is a local tool designed to find potential off-target sites in any given genome or user-provided sequence, with user-specified types of protospacer adjacent motif, and number of mismatches allowed in the seed and non-seed regions. AVAILABILITY http://eendb.zfgenetics.org/casot/ CONTACT: zfgenetics@gmail.com or bzhang@pku.edu.cn Supplementary Information: Supplementary data are available at Bioinformatics online.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/9611ba952a55b75eacda2c86ebffb7b8048251d1

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Citations in the corpus

• Evaluation of off-target and on-target scoring algorithms and integration into the guide RNA selection tool CRISPOR (2016, background): “Although published tools and scoring systems allow ranking sequences by specificity [10–22] and efficiency [2, 8, 23–25], they are usually limited to a handful of genomes and only few evidence-based recommendations exist to optimize offtarget search parameters and on-target efficiency.”