Cas-OFFinder: a fast and versatile algorithm that searches for potential off-target sites of Cas9 RNA-guided endonucleases

By Sangsu Bae, Jeongbin Park, Jin-Soo Kim. Bioinform., 2014

2,058 citations recorded by the source corpus.

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: baesau@snu.ac.kr or jskim01@snu.ac.kr

Subfields: Cellular and Molecular Neuroscience, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/bc6e1edafbc0c35c2b2239f1fc19ec15fdc3107b

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In Molecular Biology

1. Jin-Soo Kim
2. Sojung Kim
3. S. Cho
4. Daesik Kim
5. Jungeun Kim
6. Lingling Chen
7. Jim Kent
8. Maximilian Haeussler

Citations in the corpus

• Evaluation of off-target and on-target scoring algorithms and integration into the guide RNA selection tool CRISPOR (2016, methodology): “Shown are the number of mismatches in the first columns, then over three columns the number of off-targets predicted for each tool, then two columns with the number of sites found by CRISPOR and CasOffFinder but not by the MIT site, then two columns with the number of sites found by the MIT site but”
• Highly efficient RNA-guided genome editing in human cells via delivery of purified Cas9 ribonucleoproteins (2014, methodology): “A web-based computer program that can be used for the identification of such sites are available(Bae et al. 2014).”
• DeepCRISPR: optimized CRISPR guide RNA design by deep learning (2018, methodology): “Most existing tools use simple sequence alignment with different nucleotide mismatches to exhaustively search for off-target sites [20].”