Houxiang Zhu1, Chun Liang1,2. 1. Department of Biology, Miami University, Oxford, OH, USA. 2. Department of Computer Science and Software Engineering, Miami University, Oxford, OH, USA.
Abstract
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.
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.
Authors: Keunsub Lee; Yingxiao Zhang; Benjamin P Kleinstiver; Jimmy A Guo; Martin J Aryee; Jonah Miller; Aimee Malzahn; Scott Zarecor; Carolyn J Lawrence-Dill; J Keith Joung; Yiping Qi; Kan Wang Journal: Plant Biotechnol J Date: 2018-07-22 Impact factor: 9.803
Authors: Marta Vazquez-Vilar; Víctor Garcia-Carpintero; Sara Selma; Joan M Bernabé-Orts; Javier Sanchez-Vicente; Blanca Salazar-Sarasua; Arianna Ressa; Carmine de Paola; María Ajenjo; Jose Carlos Quintela; Asun Fernández-Del-Carmen; Antonio Granell; Diego Orzáez Journal: Front Plant Sci Date: 2021-07-01 Impact factor: 5.753