Eric Malekos

CRISPRware is an efficient method for generating guide RNA (gRNA) libraries against transcribed, translated, and noncoding regions. CRISPRware leverages next-generation sequencing data to design context-specific gRNAs and can account for genetic variation, which allows allele-specific guide design on a genome-wide scale.

CRISPR-Cas systems are widely used for both targeted experiments and genome-wide perturbation screens. In both cases, a successful experiment begins with choosing guide RNAs (gRNAs) complementary to the genomic target region (or protospacer) and predicted to have high on-target activity and low off-target activity. While significant attention has been paid to predicting on-target and off-target activity for a predetermined set of gRNAs, there is not a robust method for selecting gRNAs in the first place. Nor is there a tool that allows users to easily use next generation sequencing (NGS) data from genomic and transcriptomic sources to design gRNA libraries for specific cell types or experimental conditions. These challenges and shortfalls are addressed in CRISPRware, a software package that combines validated scoring techniques with rational design principles to allow users to efficiently generate libraries for single genes or entire genomes.