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

PLoS One. 2015 Apr 24;10(4):e0124633. doi: 10.1371/journal.pone.0124633. eCollection 2015.


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, 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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Binding Sites
  • CRISPR-Cas Systems*
  • Computational Biology / methods*
  • Gene Targeting / methods
  • Genomics / methods
  • Humans
  • Internet*
  • RNA, Messenger / chemistry
  • RNA, Messenger / genetics
  • Reproducibility of Results
  • Software*
  • User-Computer Interface
  • Web Browser


  • RNA, Messenger

Grant support

TT received a Postdoctoral Fellowship of the cluster of excellence CellNetworks. The project was supported by the European Research Council (JW: ManISteC) and the German Research Foundation (DFG: SFB873, JW). The authors acknowledge the financial support of the Deutsche Forschungsgemeinschaft and Ruprecht-Karls-Universität Heidelberg within the funding programme Open Access Publishing. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.