OffScan: a universal and fast CRISPR off-target sites detection tool

BMC Genomics
Yingbo CuiCanqun Yang

Abstract

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. 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. 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.

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Citations

Apr 4, 2021·International Journal of Molecular Sciences·Natalia RyczekRyszard Słomski
May 2, 2021·Horticulture Research·Xianhang WangXiping Wang
Jun 19, 2021·Molecular Biology Reports·Kirti PrasadKumarasamypet M Mohankumar

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Software Mentioned

GuideScan
DO
OFFinder
Cas
CasOT
BWA
Perl script
OpenCL
OffScan
Bowtie

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