Abstract
MOTIVATION: CRISPR imaging enables the real-time tracking of nucleic acids. Using guide RNAs (gRNAs) to direct fluorescent tags to target regions allows for precise nucleic acid monitoring via microscopy. The design of gRNAs largely affects the efficacy of CRISPR imaging. Currently, available gRNA design tools are developed primarily for gene editing, often producing individual gRNAs that target genes or regulatory elements. RESULTS: In this study, we introduce CRIBAR, a computational tool developed to systematically design single-guide RNAs (sgRNAs) for CRISPR imaging applications. CRIBAR first generates sgRNA sets optimized to maximize the number of on-target binding sites and then evaluates the potential off-target effect. The results of the in silico experiment show that CRIBAR enables CRISPR imaging in non-repetitive regions. AVAILABILITY AND IMPLEMENTATION: CRIBAR is available as a software package at https://github.com/ucfcbb/CRIBAR and as a web server at http://genome.ucf.edu/CRIBAR.