Table 2.
Algorithms for detection of off‐target effects
| Algorithm | Description | Web source | Refs. |
|---|---|---|---|
| PEM‐seq | Detection of off‐target effects. Simultaneously determines the editing efficiency and specificity of CRISPR/Cas9 | – | 46 |
| CRISPR‐PLANT v2 | CRISPRPLANT v2 detects every off‐target | https://www.genome.arizona.edu/crispr2/ | 83 |
| CCTop | Employs position‐dependent weight coefficients in their off‐target scoring algorithms | https://crispr.cos.uni-heidelberg.de | 79 |
| CROP‐IT | Scoring potential off‐target sites by the division of protospacer into three segments with weight coefficients optimized/rained with ChIP‐Seq data | https://www.adlilab.org/CROP-IT/homepage.html | 85 |
| CHOPCHOP | Rapid and easy selection of the optimal CRISPR/Cas9 or TALEN target sequences in genes from various organisms | https://chopchop.cbu.uib.no/, https://chopchop.rc.fasharvard.edu | 86 |
| CHOPCHOP v2 | Web‐based tool for GE based on TALEN and CRISPR. A powerful and intuitive tool that serves both beginners and experienced users | https://chopchop.cbu.uib.no | 138 |
| CFD score | A scoring tool for a mismatch position and sequence‐dependent off‐target | https://www.broadinstitute.org/rnai/public/analysis-tools/sgrna-design https://research.microsoft.com/en-us/projects/azimuth/ | 78 |
| Feng Zhang lab's Target Finder | Employs position‐dependent weight coefficients in their off‐target scoring algorithms | https://crispr.mit.edu/ | 18, 38 |
| CT‐Finder | Predicts genomic off‐target sites | https://bioinfolab.miamioh.edu/ct-finder | 87 |
| CRISPOR | A web‐based tool which finds gRNAs in an input sequence and ranks them according to different scores evaluating potential off‐targets in the genome and predicts on‐target activity | https://crispor.org | 44 |
| CRISPR‐GE | Expedites experimental design and analyzes mutations for genome editing based on Cpf1/CRISPR/Cas9 in various organisms including plants | https://skl.scau.edu.cn/ | 89 |
| An ensemble learning method | Predicts the off‐target sites of sgRNAs | https://github.com/penn‐hui/OfftargetPredict | 48 |
| Cas‐OFFinder | Searches the potential off‐target sites in user‐defined sequences or given genome | https://www.rgenome.net/cas-offinder/ | 77 |
| MD | Analysis of the molecular function of CRISPR/Cas9 | – | 139 |