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CRISPR/Cas tools

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Computer software that aids design of guide RNAs for CRISPR gene editing

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 References
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

References

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