CCTop: An Intuitive, Flexible and Reliable CRISPR/Cas9 Target Prediction Tool

By M. Stemmer, T. Thumberger, Maria del Sol Keyer, Joachim Wittbrodt, J. L. Mateo. PLoS ONE, 2015

936 citations recorded by the source corpus.

Engineering of the CRISPR/Cas9 system has opened a plethora of new opportunities for site-directed mutagenesis and targeted genome modification. Fundamental to this is a stretch of twenty nucleotides at the 5’ end of a guide RNA that provides specificity to the bound Cas9 endonuclease. Since a sequence of twenty nucleotides can occur multiple times in a given genome and some mismatches seem to be accepted by the CRISPR/Cas9 complex, an efficient and reliable in silico selection and evaluation of the targeting site is key prerequisite for the experimental success. Here we present the CRISPR/Cas9 target online predictor (CCTop, http://crispr.cos.uni-heidelberg.de) to overcome limitations of already available tools. CCTop provides an intuitive user interface with reasonable default parameters that can easily be tuned by the user. From a given query sequence, CCTop identifies and ranks all candidate sgRNA target sites according to their off-target quality and displays full documentation. CCTop was experimentally validated for gene inactivation, non-homologous end-joining as well as homology directed repair. Thus, CCTop provides the bench biologist with a tool for the rapid and efficient identification of high quality target sites.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/e53c4e1c95c36d4b56055fdcca679da551178199

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Citations in the corpus

DeepCRISPR: optimized CRISPR guide RNA design by deep learning (2018, methodology): “As a result, our final trained off-target site prediction model was tested on the independent datasets for each of the two cell lines and compared with four of the current state-of-the-art off-target site prediction tools, CFD score [2], MIT score [6], CROP-IT [45], and CCTop [46] .”
In Silico Predictive Modeling of CRISPR/Cas9 guide efficiency (2015, methodology): “The CCTop algorithm 13 creates off-target scores based on a simple function of distance to the PAM, and then combines these to obtain a target site score, which is then combined with distance to the PAM and other factors to yield a final score.”
Evaluation of off-target and on-target scoring algorithms and integration into the guide RNA selection tool CRISPOR (2016, methodology): “Stemmer M, Thumberger T, Del Sol KM, Wittbrodt J, Mateo JL. CCTop: an intuitive, flexible and reliable CRISPR/Cas9 target prediction tool.”