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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Ultrafast and memory-efficient alignment of short DNA sequences to the human genome.
Langmead, B., Trapnell, C., Pop, M., & Salzberg, S. L. (2009) · Genome Biology · doi:10.1186/gb-2009-10-3-r25 · Cited by 21,849
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Jinek, M., Chylinski, K., Fonfara, I., Hauer, M., Doudna, J. A., & Charpentier, E. (2012) · Science · doi:10.1126/science.1225829 · Cited by 17,116
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Cong, L., Ran, F. A., Cox, D., Lin, S., Barretto, R., Habib, N., Hsu, P. D., Wu, X., Jiang, W., Marraffini, L. A., et al. (2013) · Science · doi:10.1126/science.1231143 · Cited by 15,339
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Kent, W. J., Sugnet, C. W., Furey, T. S., Roskin, K. M., Pringle, T. H., Zahler, A. M., & Haussler, A. D. (2002) · Genome Research · doi:10.1101/gr.229102 · Cited by 10,400
RNA-Guided Human Genome Engineering via Cas9
Mali, P., Yang, L., Esvelt, K. M., Aach, J., Guell, M., DiCarlo, J. E., Norville, J. E., & Church, G. M. (2013) · Science · doi:10.1126/science.1232033 · Cited by 9,210
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Hsu, P. D., Scott, D. A., Weinstein, J. A., Ran, F. A., Konermann, S., Agarwala, V., Li, Y., Fine, E. J., Wu, X., Shalem, O., et al. (2013) · Nature Biotechnology · doi:10.1038/nbt.2647 · Cited by 4,741
Efficient genome editing in zebrafish using a CRISPR-Cas system
Hwang, W. Y., Fu, Y., Reyon, D., Maeder, M. L., Tsai, S. Q., Sander, J. D., Peterson, R. T., Yeh, J.-R. J., & Joung, J. K. (2013) · Nature Biotechnology · doi:10.1038/nbt.2501 · Cited by 2,937
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Miller, J. C., Tan, S., Qiao, G., Barlow, K. A., Wang, J., Xia, D. F., Meng, X., Paschon, D. E., Leung, E., Hinkley, S. J., et al. (2011) · Nature Biotechnology · doi:10.1038/nbt.1755 · Cited by 2,098

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Afzal, S., Sirohi, P., & Singh, N. K. (2020) · Biotechnology Letters · doi:10.1007/s10529-020-02950-w · Cited by 51
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Unlocking HDR-mediated nucleotide editing by identifying high-efficiency target sites using machine learning
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Queuosine‐tRNA promotes sex‐dependent learning and memory formation by maintaining codon‐biased translation elongation speed
Cirzi, C., Dyckow, J., Legrand, C., Schott, J., Guo, W., Pérez-Hernández, D., Hisaoka, M., Parlato, R., Pitzer, C., van der Hoeven, F., et al. (2023) · The EMBO Journal · doi:10.15252/embj.2022112507 · Cited by 45

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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