Introduction

Although the CRISPR/Cas9/sgRNA system efficiently cleaves intracellular DNA at desired target sites, major concerns remain on potential "off-target" cleavage that may occur throughout the whole genome. In order to improve CRISPR-Cas9 specificity for targeted genome editing and transcriptional control, we describe a bioinformatics tool "sgRNAcas9", which is a software package developed for fast design of CRISPR sgRNA with minimized off-target effects. This package consists of programs to perform a search for CRISPR target sites (protospacers) with user-defined parameters, predict genome-wide Cas9 potential off-target cleavage sites (POT), classify the POT into three categories, batch-design oligonucleotides for constructing 20-nt (nucleotides) or truncated sgRNA expression vectors, extract desired length nucleotide sequences flanking the on- or off-target cleavage sites for designing PCR primer pairs to validate the mutations by T7E1 cleavage assay. Importantly, by identifying potential off-target sites in silico, the sgRNAcas9 allows the selection of more specific target sites and aids the identification of bona fide off-target sites, significantly facilitating the design of sgRNA for genome editing applications. sgRNAcas9 software package is publicly available at BiooTools website (www.biootools.com) under the terms of the GNU General Public License.

Publications

  1. sgRNAcas9: a software package for designing CRISPR sgRNA and evaluating potential off-target cleavage sites.
    Cite this
    Xie S, Shen B, Zhang C, Huang X, Zhang Y, 2014-01-01 - PloS one

Credits

  1. Shengsong Xie
    Developer

    Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, China

  2. Bin Shen
    Developer

    MOE Key Laboratory of Model Animal for Disease Study, Model Animal Research Center of Nanjing University, China

  3. Chaobao Zhang
    Developer

    Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, China

  4. Xingxu Huang
    Developer

    MOE Key Laboratory of Model Animal for Disease Study, Model Animal Research Center of Nanjing University, China

  5. Yonglian Zhang
    Investigator

    Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, China

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Summary
AccessionBT001246
Tool TypeApplication
Category
PlatformsLinux/Unix
TechnologiesPerl
User InterfaceTerminal Command Line
Download Count0
Country/RegionChina
Submitted ByYonglian Zhang