Table 2.

Computational tools for designing guide RNAs.

Name	Website	Specificity Score	Genomes Supported	Single / Paired Design	Cas9 Orthologs Supported	Custo m Guide Length	Lists Off Targets	Considers Off Targets with Indels
Benchling	http://benchling.com	(Hsu et al., 2013)	22	Both	5	Yes	Yes	No
BLAST (on predesigned guide)	http://blast.ncbi.nlm.nih.gov/Blast.cgi	Sequence similarity	1000+	N/A	N/A	Yes	Yes	Yes
Cas-OFFinder	http://www.rgenome.net/cas-offinder/	No	34	Single	4	Yes	Yes	Yes
MIT CRISPR Design Tool	CRISPR.mit.edu	(Hsu et al., 2013)	16	Both	1	No	Yes	No
Deskgen	http://deskgen.com	(Hsu et al., 2013)	5	Both	4	Yes	Yes	No
DNA 2.0 CRISPR gRNA Design Tool	https://www.dna20.com/eCommerce/cas9/input	Relative ranking based on orthogonality	5	Both	1	No	No	No
E-CRISP	http://www.e-crisp.org/E-CRISP/designcrispr.html	Relative ranking based on orthogonality	34	Both	1	Yes	Yes	No
EuPaGDT	https://grna.ctegd.uga.edu	Relative ranking based on orthogonality	28	Single	Custom PAM	Yes	Yes	No
GenScript gRNA Design Tool	http://www.genscript.com/gRNA-design-tool.html	No	2	Single	1	Yes	No	No
ZiFiT	http://zifit.partners.org/ZiFiT/Disclaimer.aspx	Orthogonality of Offtargets	9	Both	1	Yes	Yes	No
Broad GPP Portal	http://www.broadinstitute.org/rnai/public/analysis-tools/sgrna-design	Cutting Frequency Determination (CFD) (Doench et al., 2016)	2	Single	1	No	No	Yes
CROP-IT	http://cheetah.bioch.virginia.edu/AdliLab/CROP-IT/	(Singh et al., 2015)	2	Both	1	No	Yes	No