CRISPcut: A novel tool for designing optimal sgRNAs for CRISPR/Cas9 based experiments in human cells.
The ability to direct the CRISPR/Cas9 nuclease to a unique target site within a genome would have broad use in targeted genome engineering. However, CRISPR RNA is reported to bind to other genomic locations that differ from the intended target site by a few nucleotides, demonstrating significant off-target activity. We have developed the CRISPcut tool that screens the off-targets using various parameters and predicts the ideal genomic target for -guide RNAs in human cell lines. sgRNAs for four different types of Cas9 nucleases can be designed with an option for the user to work with different PAM sequences. Direct experimental measurement of genome-wide DNA accessibility is incorporated that effectively restricts the prediction of CRISPR targets to open chromatin. An option to predict target sites for paired CRISPR nickases is also provided. The tool has been validated using a dataset of experimentally used sgRNA and their identified off-targets. URL: http://web.iitd.ac.in/crispcut.
['Dhanjal|Jaspreet Kaur|JK|', 'Radhakrishnan|Navaneethan|N|', 'Sundar|Durai|D|']
D000076987:CRISPR-Associated Protein 9 D064113:CRISPR-Cas Systems D002843:Chromatin D000072669:Gene Editing D006801:Humans D059372:Nucleotide Motifs D017394:RNA, Guide D012984:Software D052416:Targeted Gene Repair
sgRNA CRISPRs Cas9 Genome engineering Protospacer adjacent motif