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CCTop: An Intuitive, Flexible and Reliable CRISPR/Cas9 Target Prediction Tool
Open accessAbstract
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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“CCTop and CROP-IT generate scores based on the distances of the mismatches to the PAM (Singh et al., 2015; Stemmer et al., 2015).”
From Off-target effects in CRISPR/Cas9 gene editing (2023) · cites this paper as Stemmer et al., 2015
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Metadata
- 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.
- Venue
- PLoS ONE
- Publisher
- Public Library of Science (PLoS)
- Published
- 2015-04-24
- Volume
- 10
- Issue
- 4
- Pages
- e0124633
- ISSN
- 1932-6203 (ISSN-L)
- 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
- 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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