CCTop - CRISPR/Cas9 target online predictor

Time 2020-10-02 17:04:25

Web Name: CCTop - CRISPR/Cas9 target online predictor

WebSite: http://crispr.cos.uni-heidelberg.de

ID:67834

Keywords:

CRISPR,CCTop,predictor,

Description:

5 limitation PAM 5'NNNNNNNNNNNNNNNNNNNNNGG 3 limitation (In vitro) transcription depends on a leading 'G' (U6 promoter) or 'GG' (T7 promoter). However, it was shown that the leading guanin(s) can also be added or substituted at the 5' end of any sgRNA target site, hence 'NN' is set as default. Hwang et al., PLoS One, (2013) Ansai & Kinoshita, Biol. Open (2014) A recent paper in C. elegans demonstrated that a ‚GG’ motif adjacent to the PAM could be beneficial for DSB introduction. Farboud & Meyer, Genetics (2015). Select your in vitro transcription method. We will provide the forward and reverse oligos to clone each candidate sgRNA into the appropriate vector. If you select "Custom" you can specify your overhangs, which will be appended to the 5' of the sgRNA sequence. Maximum number of mismatches taken into account for prediction of potential sgRNA off-target sites. Note: more than four mismatches in total will most likely prevent DSB induction. Hsu et al., Nat. Biotechnol. (2013) Cho et al., Genome Res. (2014) adjust mismatch values! core length Check to enable the 'core parameter'. More than two mismatches in the first 8-14 nucleotides adjacent to the PAM were demonstrated to abolish Cas9 mediated DSB introduction. The 'core' is a simplified parameter to account for these findings. Cong et al., Science (2013) Hsu et al., Nat. Biotechnol. (2013) Cho et al., Genome Res. (2014) : max. core mismatches Maximum number of mismatches to be allowed in the core region of potential sgRNA off-target sites. Note: more than two mismatches in total will most likely prevent DSB induction. Hsu et al., Nat. Biotechnol. (2013) Cho et al., Genome Res. (2014) If you use this tool for your scientific work, please cite it as: Stemmer, M., Thumberger, T., del Sol Keyer, M., Wittbrodt, J. and Mateo, J.L. CCTop: an intuitive, flexible and reliable CRISPR/Cas9 target prediction tool. PLOS ONE (2015). doi: 10.1371/journal.pone.0124633 If you use the CRISPRater score to select your target sites please cite as well this work: Labuhn, M., Adams, F. F., Ng, M., Knoess, S., Schambach, A., Charpentier, E. M., … Heckl, D. Refined sgRNA efficacy prediction improves large- and small-scale CRISPR–Cas9 applications. Nucleic Acids Research (2017). doi: 10.1093/nar/gkx1268

TAGS:CRISPR CCTop predictor 

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