title: CCTop: An Intuitive, Flexible and Reliable CRISPR/Cas9 Target Prediction Tool.
abstract: 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.
authors.affiliation: Centre for Organismal Studies (COS), Heidelberg University, Heidelberg, Germany.
authors.forename: Manuel
authors.initials: M
authors.lastname: Stemmer
authors.affiliation: Centre for Organismal Studies (COS), Heidelberg University, Heidelberg, Germany.
authors.forename: Thomas
authors.initials: T
authors.lastname: Thumberger
authors.affiliation: Centre for Organismal Studies (COS), Heidelberg University, Heidelberg, Germany.
authors.forename: Maria
authors.initials: M
authors.lastname: Del Sol Keyer
authors.affiliation: Centre for Organismal Studies (COS), Heidelberg University, Heidelberg, Germany.
authors.forename: Joachim
authors.initials: J
authors.lastname: Wittbrodt
authors.affiliation: Centre for Organismal Studies (COS), Heidelberg University, Heidelberg, Germany.
authors.forename: Juan L
authors.initials: JL
authors.lastname: Mateo
mesh_terms: D000818:Animals; D001665:Binding Sites; D064113:CRISPR-Cas Systems; D019295:Computational Biology / Q000379:methods*; D018390:Gene Targeting / Q000379:methods; D023281:Genomics / Q000379:methods; D006801:Humans; D020407:Internet; D012333:RNA, Messenger / Q000737:chemistry / Q000235:genetics; D015203:Reproducibility of Results; D012984:Software; D014584:User-Computer Interface; D064878:Web Browser
chemical_list: D012333:RNA, Messenger