Table 2.
Commonly used gRNA design tools.
| Tool | Organism | Language | Cas Nucleases | Description | Database/ Web Server |
Web Site (Accessed on 10 November 2022) |
Ref. |
|---|---|---|---|---|---|---|---|
| CHOP CHOP | More than 100 | Python | Cas9, Cas12, Cas13 | Early web-based tool created by Harvard University to design gRNA based on matches and mismatches | Web server | http://crispor.tefor.net/ | [36] |
| CRISPR RGNE tools | More than 100 | Python | More than 20 Cas nucleases | Predicts multiple off-target and on-target effects based on the Cas-OFFinder model | Web server | http://www.rgenome.net/cas-designer/ | |
| CRISTA | More than 100 | Pearl and Python | Only Cas9 | Machine learning (ML)-based tools to predict off-target and on-target effects simultaneously | Web server | [35] | |
| GuideScan | Mouse and human | Python | Cpf1 and Cas9 | Predicts off-target effects based on sequence and structural features | Web server | https://guidescan.com/ | [37] |
| CRISPRDo | Human, mouse, zebrafish, and some worm species | Python | Cas9 and Cpf1 | Predict off-target and on-target effects simultaneously | Database | [38] | |
| sgRNACas9 | Mouse | Pearl | spCas9 | A web-based tool to predict off-target effects | Dataset | [39,40] | |
| EupaDGT | Eukaryotic pathogen | Python | More than 10 Cas nucleases | Machine-learning-based tool to predict on- and off-target effects simultaneously | Web-based | http://grna.ctegd.uga.edu/ | [41] |
| WU-CRISPR | Human and mouse | Pearl | SpCas9 | Machine-learning-algorithm-based tool that can predict off-target effects by providing sequences between 20 and 30,000 bp | Web-based | http://crispr.wustl.edu/ | [42] |
| CRISPR-P | 49 plant species | Python | More than 14 Cas nucleases orthologs | Web-based off-target and on-target prediction tools for a wide range of plant species | Web-based | http://crispr.hzau.edu.cn/CRISPR2 | [43] |
| CRISPRz | Zebrafish, human, and mouse | Python | spCas9 | Trained on large datasets from zebrafish, humans, and mice to generate a gRNA dataset | Web-based | https://research.nhgri.nih.gov/CRISPRz/ | [44] |
| PhytoCRISPR x | Wide range of plant species and especially phytoplankton | Pearl/bash | SpCas9. Cas12 | Web-based tool to predict off-target effects | Dataset | [46] | |
| CRISPRPOR | More than 100 species | Python | More than 30 Cas orthologs | Design gRNA dataset based on match/match in seed regions | Web tool | http://crispor.tefor.net/ | [45] |
| Png Designer | 6 | Python | Cas9 | A newly designed tool for generating guide RNA for base editing and prime editing | Web tool | https://www.crisprindelphi.design/ | [47] |