TABLE 5.

The most popular alignment-based methods and related search engines.

Search engine	Methods
BLAST	CRISPRTarget (Biswas et al., 2013), CRISPR-P (Liu et al., 2017), and CRISPR-GA (Luyten et al., 2004)
BOWTIE	CRISPR-ERA (Liu et al., 2015), CHOPCHOP (Labun et al., 2019), CasFinder (Upadhyay and Sharma, 2014), CCTop (Stemmer et al., 2015), E-CRISP (Heigwer et al., 2014), and CLD (Heigwer et al., 2016)
BWA	CRISPR-DO (Ma et al., 2016), CRISPOR (Concordet and Haeussler, 2018), and CRISPETa (Pulido-Quetglas et al., 2017)
BRUTE FORCE	GuideScan (Perez et al., 2017), Cas-OFFinder (Bae et al., 2014), FlashFry (McKenna and Shendure, 2018), Crisflash (Jacquin et al., 2019), CRISPRitz (Cancellieri et al., 2020), and CRISPR-SE (Li et al., 2021)