Table 1.
CRISPR/Cas9 sgRNA Design Tools
| Tool Name | Provider | Searches whole genome for targets | Returns all targets of genome | Seed span and location can be defined | Maximum number of mismatches supported | Predicts gRNA activity | Available PAM sequences | gRNA suggestion or scoring |
|---|---|---|---|---|---|---|---|---|
| Benchling CRISPR gRNA Design | Benchling | Yes | Yes | Yes | 4 | Yes | User customizable | Yes |
| Breaking-Cas | Spanish National Center for Biotechnology | Yes | Yes | Yes | 4 | No | User customizable | Yes |
| Cas-OFFinder | Seoul National University | Yes | Yes | No | 0–10 | No | NGG, NRG, NNAGAAW, NNNNGMTT | Yes |
| CCTop | University of Heidelberg | Yes | Yes | Partial | 5 (0–5) | No | NGG, NRG, NNGRRT, NNNNGATT, NNAGAAW, NAAAAC | Yes |
| CHOPCHOP | Harvard University | Yes | Yes | Partial | 0, 2 | No | NGG, NNAGAA, NNNNGANN | Yes |
| CHOPCHOP v2 | University of Bergen | Yes | Yes | Yes | 3 (0–3) | Yes | User customizable | Yes |
| COD | Dayong Guo | No | No | No | 0, 3, 5, 8 | No | NGG and NAG | Yes |
| CRISPR Configurator & Specificity Tool | Dharmacon, Inc. | Yes (over 30 species) | Yes | Yes | 8 (gaps or mismatches) | Internally | NGG and NAG | No |
| CRISPR Design | Zhang Lab, MIT | Yes | No | No | 4 | No | NGG and NAG | Yes |
| CRISPRdirect | Database Center for Life Science (DBCLS) | Yes (over 200 species) | Yes | No | Any number | No | NNN | Yes |
| CRISPR gRNA Design Tool | DNA2.0 | Yes | Yes | No | 0–10 | No | NGG, NAG | Yes |
| CRISPRseek | Bioconductor | Yes | Yes | No | Any number | No | User customizable | Yes |
| DESKGEN | Desktop Genetics | Yes | Yes | Yes | Any number | Yes | Fully user customizable | Yes |
| Off-Spotter | Thomas Jefferson University | Yes | Yes | Yes | 0–5 | Yes | NGG, NAG, NNNNACA, NNGRRT (R is A or G) | User customizable |
| sgRNA Designer | Broad Institute | No | No | No | 0 | Yes | NGG | Yes |