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. __TOC__
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 supportedPredicts gRNA activity Available Protospacer adjacent motif (PAM) sequences Annotation is reported gRNA suggestion or scoring CRISPRon, CRISPRoffCenter for non-coding RNA in Technology and Health, University of CopenhagenYesYesYesAllYesNGG, NGA, NAGYesYes,Invitrogen TrueDesign Genome EditorThermo Fisher ScientificYesYesNo3NoNGGYesYesBreaking-CasSpanish National Center for BiotechnologyYes (over 1000 genomes)YesYes (by weights)4NoUser customizableYesYes Cas-OFFinder Seoul National University Yes Yes No 0-10No NGG, NRG, NNAGAAW, NNNNGMTT No Yes CASTINGCaagleYesYesNo3NoNGG and NAGNoYesCRISPy 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, 2No 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 4Yes NGG, NGA, NGCG, NNAGAA, NGGNG, NNGRRT, NNNRRT, NNNNGMTT, NNNNACA, TTTN Yes Yes CRISPR Design Zhang Lab, MIT Yes No No 4No NGG and NAG mRNA exons Yes CRISPRdirect Database Center for Life Science (DBCLS) Yes (over 200 species) Yes No Any numberNo NNN Yes Yes CRISPRscan Giraldez Lab, Yale Yes Yes No 4Yes NGG, TTTV, TTTN Yes Yes CRISPRseek Bioconductor Yes Yes No Any numberNo User customizable mRNA exons Yes DESKGEN Desktop Genetics Yes Yes Yes Any numberYes Fully user customizable Yes Yes GuideScan GuideScan Yes Yes Yes 3 on website and customizable with command lineYes NGG/NAG on website and customizable with command line Yes Yes GT-ScanCSIRO & YesYesYes3 (0-3)NoUser customizableLinks to Ensembl genome browserYes 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 0Yes NGG CDS (if searching by transcript ID) Yes Synthego Design ToolSynthegoYes (over 120,000 genomes)No (Optimized for Knockout)Yes3YesNGGYes (RefSeq, Ensembl, Gencode)YesTechCrunch. "Synthego's genetic toolkit aims to make CRISPR more accessible | May 2017" Retrieved 23 January 2018.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 DesignerHorizon DiscoveryYes, Multipleyesyes4YesNGG, NNGRRT, YTTV, otherYesYes(21)GuideMakerUnited States Department of Agriculture, Agricultural Research ServiceYes, any user supplied genomeYesYes0-5YesAny PAM site and PAM orientationYesYesWGEWellcome Sanger InstituteYes, human and mouse reference genomesYesYes4 (0-4)NoNGGYesYes
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