# CRISPR/Cas tools

CRISPR-Cas design tools are computer software platforms and bioinformatics tools used to facilitate the design of guide RNAs (gRNAs) for use with the CRISPR/Cas gene editing system.

## CRISPR-Cas

The CRISPR/Cas (clustered regularly interspaced short palindromic repeats/CRISPR associated nucleases) system was originally discovered to be an acquired immune response mechanism used by archaea and bacteria. It has since been adopted for use as a tool in the genetic engineering of higher organisms.
Designing an appropriate gRNA is an important element of genome editing with the CRISPR/Cas system. A gRNA can and at times does have unintended interactions ("off-targets") with other locations of the genome of interest. For a given candidate gRNA, these tools report its list of potential off-targets in the genome thereby allowing the designer to evaluate its suitability prior to embarking on any experiments.
Scientists have also begun exploring the mechanics of the CRISPR/Cas system and what governs how good, or active, a gRNA is at directing the Cas nuclease to a specific location of the genome of interest. As a result of this work, new methods of assessing a gRNA for its 'activity' have been published, and it is now best practice to consider both the unintended interactions of a gRNA as well as the predicted activity of a gRNA at the design stage.

## Table

The below table lists available tools and their attributes.
List of CRISPR-Cas 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 Protospacer adjacent motif (PAM) sequences | Annotation is reported | gRNA suggestion or scoring | Ref. |
| CRISPRon, CRISPRoff | Center for non-coding RNA in Technology and Health, University of Copenhagen | Yes | Yes | Yes | All | Yes | NGG, NGA, NAG | Yes | Yes | , |
| Invitrogen TrueDesign Genome Editor | Thermo Fisher Scientific | Yes | Yes | No | 3 | No | NGG | Yes | Yes | |
| Breaking-Cas | Spanish National Center for Biotechnology | Yes (over 1000 genomes) | Yes | Yes (by weights) | 4 | No | User customizable | Yes | Yes | |
| Cas-OFFinder | Seoul National University | Yes | Yes | No | 0-10 | No | NGG, NRG, NNAGAAW, NNNNGMTT | No | Yes | |
| CASTING | Caagle | Yes | Yes | No | 3 | No | NGG and NAG | No | Yes | |
| CRISPy | Technical University of Denmark | Yes | Yes | No | All | No | NGG | Yes | Yes | |
| CCTop | University of Heidelberg | Yes | Yes | Partial | 5 (0-5) | Yes | NGG, NRG, NNGRRT, NNNNGATT, NNAGAAW, NAAAAC | Yes | Yes | |
| CHOPCHOP | Harvard University | Yes | Yes | Partial | 0, 2 | No | NGG, NNAGAA, NNNNGANN | No | Yes | |
| CHOPCHOP v2 | University of Bergen | Yes | Yes | Yes | 3 (0-3) | Yes | User customizable | Yes | Yes | |
| CRISPOR | University of California, Santa Cruz TEFOR | Yes (over 200 genomes) | Yes | No | 4 | Yes | NGG, NGA, NGCG, NNAGAA, NGGNG, NNGRRT, NNNRRT, NNNNGMTT, NNNNACA, TTTN | Yes | Yes | |
| CRISPR Design | Zhang Lab, MIT | Yes | No | No | 4 | No | NGG and NAG | mRNA exons | Yes | |
| CRISPRdirect | Database Center for Life Science (DBCLS) | Yes (over 200 species) | Yes | No | Any number | No | NNN | Yes | Yes | |
| CRISPRscan | Giraldez Lab, Yale | Yes | Yes | No | 4 | Yes | NGG, TTTV, TTTN | Yes | Yes | |
| CRISPRseek | Bioconductor | Yes | Yes | No | Any number | No | User customizable | mRNA exons | Yes | |
| DESKGEN | Desktop Genetics | Yes | Yes | Yes | Any number | Yes | Fully user customizable | Yes | Yes | |
| GuideScan | GuideScan | Yes | Yes | Yes | 3 on website and customizable with command line | Yes | NGG/NAG on website and customizable with command line | Yes | Yes | |
| GT-Scan | CSIRO & EMBL-ABR | Yes | Yes | Yes | 3 (0-3) | No | User customizable | Links to Ensembl genome browser | Yes | |
| Off-Spotter | Thomas Jefferson University | Yes | Yes | Yes | 0-5 | | NGG, NAG, NNNNACA, NNGRRT (R is A or G) | mRNA exons, unspliced mRNA, mRNA, 5'UTR, CDS, 3'UTR, unspliced lincRNA, lincRNA | User customizable | |
| sgRNA Designer | Broad Institute | No | No | No | 0 | Yes | NGG | CDS (if searching by transcript ID) | Yes | |
| Synthego Design Tool | Synthego | Yes (over 120,000 genomes) | No (Optimized for Knockout) | Yes | 3 | Yes | NGG | Yes (RefSeq, Ensembl, Gencode) | Yes | |
| TUSCAN | CSIRO | No | No | No | 0 | Yes | NGG | No | Yes | |
| VARSCOT | CSIRO | Yes | Yes | No | 0-8 | Yes | User customizable | No | Yes | |
| CRISPR Targeted Gene Designer | Horizon Discovery | Yes, Multiple | yes | yes | 4 | Yes | NGG, NNGRRT, YTTV, other | Yes | Yes | (21) |
| GuideMaker | United States Department of Agriculture, Agricultural Research Service | Yes, any user supplied genome | Yes | Yes | 0-5 | Yes | Any PAM site and PAM orientation | Yes | Yes | |
| WGE | Wellcome Sanger Institute | Yes, human and mouse reference genomes | Yes | Yes | 4 (0-4) | No | NGG | Yes | Yes | |