Application of Bioinformatics Tools in CRISPR/Cas

Abstract

Clustered regularly interspaced short palindromic repeats (CRISPR) target sequence selection is a key step for achieving successful targeted gene editing. Possible off-target editing and variance in editing efficacy imposes restrictions on target site selection. In recent years, for conducting CRISPR knock-in/out experiments, a plethora of computational tools have been developed to aid researchers in target site selection. These tools are likely to help in selecting the target site and in designing highly specific single-guide RNA (sgRNA) for CRISPR applications. The broadening of CRISPR applications has also seen the development of sgRNA design tools specifically for CRISPR-mediated gene regulation and genetic screening studies. Besides assisting in sgRNA design, computational tools have been developed to evaluate CRISPR genome-edited data generated through Next Generation Sequencing (NGS) platforms. The computational tools developed have their own salient features, differ in design specifications, input parameters, genomes, output data and visualisation. Therefore, it is important for researchers to choose the appropriate tools suitable for their experimental design. In this chapter, we have comprehensively outlined the various sgRNA design tools available in plants for use in different CRISPR applications and their on-target efficiency prediction models and off-target detection. These models provide us an insight into the underlying criteria used while developing CRISPR tools. We also discuss computational tools developed for genome editing assessment using NGS data. This chapter walks the reader through a collection of computational tools along with their features available for CRISPR applications, especially in the context of plants. We hope that this compiled information on CRISPR bioinformatics tools would benefit plant scientists while performing their CRISPR/Cas experiment.