TABLE 1.
In silico tools for off-target prediction.
| Tool | Method | Advantages | Disadvantages |
|---|---|---|---|
| CasOT Xiao et al. (2014) | Alignment | User-defined PAM and number of mismatches | Slow speed output. Bulges are not allowed |
| Cas-OFFinder Bae et al. (2014) | Alignment | User-defined PAM, sgRNA length and number of mismatches. Allows bulges | Moderate speed output |
| FlashFry McKenna and Shendure, (2018) | Alignment | User-defined PAM and number of mismatches. High speed output. Suitable for large datasets | Bulges are not allowed |
| Crisflash Jacquin et al. (2019) | Alignment | User-defined PAM and number of mismatches. High speed output | Bulges are not allowed |
| MIT Hsu et al. (2013) | Scoring | Good ranking performance. Web platform, implemented in the CRISPOR website Haeussler et al. (2016) | Scorings are outperformed by more recent tools. Bulges are not allowed |
| CROP-IT Singh et al. (2015) | Scoring | Web platform. Good ranking performance Haeussler et al. (2016) | Scorings are outperformed by more recent tools |
| CFD Doench et al. (2016) | Scoring | Based on experimental datasets. Very good ranking performance Haeussler et al. (2016) | Requires command line |
| DeepCRISPR Chuai et al. (2018) | Scoring | Based on experimental datasets. Very good ranking performance. Includes both sequence and epigenetic features | Requires command line. On-target training data may contain noise. Does not take into account indels relative to the sgRNA target sequence |