Jack Lin's CRISPR/Cas9 gRNA finder

Sequence Name (optional): leading gRNA length:


Paste the sequence that you would like to search for CRISPR/Cas9 gRNA mediated genome editing, and leading gRNA length is the number of base pairs before NGG(PAM, the protospacer adjacent motif). After getting your results, you will be able to blast them, BLAT them and check secondary structures directly without copy&paste! This gRNA finder only checks for the sense strand, please do reverse compliment somewhere else if you want to check gRNA in the antisense strand.

Please check following references for good designing of your own gRNA:

Mali P, Yang L, Esvelt KM, Aach J, Guell M, DiCarlo JE, Norville JE, Church GM. RNA-guided human genome engineering via Cas9. Science 2013 Feb 15;339(6121):823-6.

Cong L, Ran FA, Cox D, Lin S, Barretto R, Habib N, Hsu PD, Wu X, Jiang W, Marraffini LA, Zhang F. Multiplex genome engineering using CRISPR/Cas systems. Science 2013 Feb 15;339(6121):819-23.

Parisien M, Major F. The MC-Fold and MC-Sym pipeline infers RNA structure from sequence data. Nature 2008, 452(7183):51-55.

Bindewald E, Kluth T, Shapiro BA. CyloFold: secondary structure prediction including pseudoknots. Nucleic Acids Research, 2010, Vol. 38, W368-72.