CRISPR-DT: designing gRNAs for the CRISPR-Cpf1 system with improved target efficiency and specificity

MOTIVATION: The Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-Cpf1 system has been successfully applied in genome editing. However, target efficiency of the CRISPR-Cpf1 system varies among different guide RNA (gRNA) sequences. RESULTS: In this study, we reanalyzed the published CRISPR-Cpf1 gRNAs data and found many sequence and structural features related to their target efficiency. With the aid of Random Forest in feature selection, a support vector machine model was created to predict target efficiency for any given gRNAs. We have developed the first CRISPR-Cpf1 web service application, CRISPR-DT (CRISPR DNA Targeting), to help users design optimal gRNAs for the CRISPR-Cpf1 system by considering both target efficiency and specificity. CRISPR-DT will empower researchers in genome editing. AVAILABILITY AND IMPLEMENTATION: CRISPR-DT, mainly implemented in Perl, PHP and JavaScript, is freely available at http://bioinfolab.miamioh.edu/CRISPR-DT. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.