Cited by 1,088CRISPR and Genetic EngineeringRNA regulation and diseaseRNA Interference and Gene Delivery

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

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Stemmer, Manuel, Thumberger, Thomas, del Sol Keyer, Maria, Wittbrodt, Joachim, Mateo, Juan L.·2015·PLoS ONE

DOI 10.1371/journal.pone.0124633PMC PMC4409221

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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.

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Authors: Stemmer, M., Thumberger, T., del Sol Keyer, M., Wittbrodt, J., & Mateo, J. L.
Affiliations: Heidelberg University (DE)
Corresponding author: Thumberger, Thomas
Wittbrodt, Joachim
Mateo, Juan L.
ORCID: Stemmer, Manuel
Thumberger, Thomas
Wittbrodt, Joachim
Mateo, Juan L.
Venue: PLoS ONE
Publisher: Public Library of Science (PLoS)
Published: 2015-04-24
Volume: 10
Issue: 4
Pages: e0124633
ISSN: 1932-6203 (ISSN-L)
DOI: 10.1371/journal.pone.0124633
PMC: PMC4409221
OpenAlex: W1990149668
Cited by: 1,088
References: 37
Citations by year: 2026: 87 · 2025: 99 · 2024: 106 · 2023: 140 · 2022: 129 · 2021: 114 · 2020: 139 · 2019: 96 · 2018: 72 · 2017: 53 · 2016: 39 · 2015: 13
FWCI: 25.61
Type: journal article
Language: en
Update notices: correction (2017-04-20)
Open access: gold
doi.org
Licence: cc-by
creativecommons.org/licenses/by/4.0/ (vor)
Locations: PLoS ONE (publishedVersion, cc-by)
Europe PMC (PubMed Central) (publishedVersion, cc-by)
PubMed Central (publishedVersion, cc-by)
PubMed (publishedVersion)
DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion)
Figshare (submittedVersion, cc-by)
Funders: Deutsche Forschungsgemeinschaft (SFB873)
Universität Heidelberg
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › CRISPR and Genetic Engineering
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA regulation and disease
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA Interference and Gene Delivery
Keywords: CRISPR/Cas9, sgRNA design, off-target prediction, genome editing, gene inactivation, non-homologous end joining, homology-directed repair, web-based prediction tool
MeSH terms: Animals, Binding Sites, Humans, RNA, Messenger, Software, User-Computer Interface, Reproducibility of Results, Gene Targeting, Computational Biology, Internet, Genomics, CRISPR-Cas Systems, Web Browser

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

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