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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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Cites
Fiji: an open-source platform for biological-image analysis
Schindelin, J., Arganda-Carreras, I., Frise, E., Kaynig, V., Longair, M., Pietzsch, T., Preibisch, S., Rueden, C., Saalfeld, S., Schmid, B., et al. (2012) · Nature Methods · doi:10.1038/nmeth.2019 · Cited by 66,890
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
A Programmable Dual-RNA–Guided DNA Endonuclease in Adaptive Bacterial Immunity
Jinek, M., Chylinski, K., Fonfara, I., Hauer, M., Doudna, J. A., & Charpentier, E. (2012) · Science · doi:10.1126/science.1225829 · Cited by 17,116
Multiplex Genome Engineering Using CRISPR/Cas Systems
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
The Human Genome Browser at UCSC
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
DNA targeting specificity of RNA-guided Cas9 nucleases
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
Genome editing with engineered zinc finger nucleases
Urnov, F. D., Rebar, E. J., Holmes, M. C., Zhang, H. S., & Gregory, P. D. (2010) · Nature Reviews Genetics · doi:10.1038/nrg2842 · Cited by 2,285
A TALE nuclease architecture for efficient genome editing
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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Hara, H., Natsagdorj, M., Byambaa, S., & Hanazono, Y. (2023) · Methods in molecular biology · doi:10.1007/978-1-0716-3016-7_16 · Cited by 4
Zhao, L., Chen, Y.-F., Xiao, X.-M., Gao, H.-Y., Cao, J., Zhang, Z., & Guo, Z. (2023) · Horticulture Research · doi:10.1093/hr/uhad043 · Cited by 4
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Koltun, A., Silva, N. V. E., Angelotti-Mendonça, J., Marin, S. R. R., Gonçalves, L. S. A., Nepomuceno, A. L., & Mertz-Henning, L. M. (2023) · Pesquisa Agropecuária Brasileira · doi:10.1590/s1678-3921.pab2023.v58.03000 · Cited by 4
Mavrommatis, L., Zaben, A., Kindler, U., Kienitz, M., Dietz, J., Jeong, H., Böhme, P., Brand‐Saberi, B., Vorgerd, M., & Zaehres, H. (2023) · Stem Cells International · doi:10.1155/2023/9246825 · Cited by 4
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Hub, T., Cornean, A., Round, K., Fleming, T., Freichel, M., & Medert, R. (2024) · ACS Pharmacology & Translational Science · doi:10.1021/acsptsci.3c00338 · Cited by 4
Khamis, G., Chi, J., & Zhao, Q. (2024) · OBM Genetics · doi:10.21926/obm.genet.2402244 · Cited by 4
Krappinger, J. C., Gomez, C. M. A., Hoenikl, A., Schusterbauer, V., Hatzl, A.-M., Feichtinger, J., & Glieder, A. (2024) · New Biotechnology · doi:10.1016/j.nbt.2024.06.008 · Cited by 4
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Zhou, R., Seth, S. R., Reeves, J., Burns, A. H., Hsieh, C., Horn, T. W., Xue, L., & Tsai, C. (2025) · Tree Physiology · doi:10.1093/treephys/tpaf081 · Cited by 4
Kouvela, A., Ponce, J. R. J., Γιαρίμογλου, Ν., Chicher, J., Marzi, S., Stathopoulos, C., & Stamatopoulou, V. (2025) · Nucleic Acids Research · doi:10.1093/nar/gkaf599 · Cited by 4
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Plasil, S. L., Collins, V. J., Baratta, A. M., Farris, S. P., & Homanics, G. E. (2022) · Advances in Drug and Alcohol Research · doi:10.3389/adar.2022.10831 · Cited by 5
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Yusof, A., Tamizi, A. A., Zim, N., Sattar, S., Salleh, M. H. M., Azmi, N. S. A., Zainal, Z., nstitute of Systems Biology, U. K. M., Zainuddin, Z., & Samsulrizal, N. H. (2023) · Journal of Tropical Life Science · doi:10.11594/jtls.13.02.04 · Cited by 4
Simirenko, L., Cheng, J., & Blaby, I. K. (2023) · Frontiers in Bioengineering and Biotechnology · doi:10.3389/fbioe.2023.1217811 · Cited by 4
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Srivastava, V. K. (2019) · Springer eBooks · doi:10.1007/978-981-13-8499-8_19 · Cited by 4
Generation of GADD45A gene knockout human embryonic stem cell line using CRISPR/Cas9
Li, J., Li, Y., Zhan, X.-Y., Ran, X., Tse, H., Dang, S., Nie, Y., & Huang, K. (2020) · Stem Cell Research · doi:10.1016/j.scr.2020.102090 · Cited by 4
Use of Mathematical Methods for the Biosafety Assessment of Agricultural Crops
Korotkov, E., Yakovleva, I. V., & Kamionskaya, A. M. (2021) · Applied Biochemistry and Microbiology · doi:10.1134/s000368382102006x · Cited by 4
CRISPR-Cas Based Precision Breeding in Date Palm: Future Applications
Sattar, M. N., Iqbal, Z., & Al-Khayri, J. M. (2021) · Compendium of plant genomes · doi:10.1007/978-3-030-73750-4_9 · Cited by 5
Cheung, N. K. M., Nakamura, R., Uno, A., Kumagai, M., Fukushima, H. S., Morishita, S., & Takeda, H. (2017) · PLoS Genetics · doi:10.1371/journal.pgen.1007123 · Cited by 4
Wan, H., Li, J., Ding, H., Lin, S., Tu, S., Tian, X.-H., Hu, J., & Chang, S. (2019) · Protein and Peptide Letters · doi:10.2174/0929866526666191028162302 · Cited by 4
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Eslami-Mossallam, B., Klein, M., van der Smagt, C. P., van der Sanden, K., Jones, S. K., Hawkins, J. A., Finkelstein, I. J., & Depken, M. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.05.21.108613 · Cited by 4
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Fiaz, S., Khan, S. A., Anis, G. B., Ali, H., Ali, M., Ali, K., Noor, M. A., Ahmad, S., & Asad, B. A. (2021) · Wiley eBooks · doi:10.1002/9781119672425.ch3 · Cited by 5
Zhang, Z., Chen, N., Liu, R., Yin, N., He, Y., Li, D., Tong, M., Gao, A., Lu, P., Li, H., et al. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.08.13.456245 · Cited by 4
Negative DNA Supercoiling Induces Genome Wide Cas9 Off-Target ActivityPreprint
Newton, M. D., Losito, M., Smith, Q. M., Parnandi, N., Taylor, B. J., Akçakaya, P., Maresca, M., Wang, Y.-F., Boulton, S. J., King, G. A., et al. (2022) · SSRN Electronic Journal · doi:10.2139/ssrn.4199637 · Cited by 4
Kaul, T., Verma, R., Sony, S. K., Bharti, J., Motelb, K. F. A., Prakash, A. T., Kaul, R., Nehra, M., & Eswaran, M. (2023) · Wiley eBooks · doi:10.1002/9781119858553.ch9 · Cited by 5
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Welz, B., Pierotti, S., Fitzgerald, T., Thumberger, T., Suzuki, R., Watson, P., Fuss, J., da Trindade, T. C., Defranoux, F., Ferreira, M., et al. (2026) · Cell Genomics · doi:10.1016/j.xgen.2026.101164 · Cited by 5
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Fukunaga, T., Iwakiri, J., & Hamada, M. (2023) · Methods in molecular biology · doi:10.1007/978-1-0716-2768-6_11 · Cited by 3
Zeder‐Lutz, G., Bornert, O., Fellmann-Clauss, R., Knittel-Obrecht, A., Tranchant, T., Bouteben, S., Kaeffer, J., Quillet, R., Villa, P., Wagner, R., et al. (2023) · Analytical Biochemistry · doi:10.1016/j.ab.2023.115062 · Cited by 3
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Guan, Z., & Jiang, Z. (2024) · Computers in Biology and Medicine · doi:10.1016/j.compbiomed.2024.108781 · Cited by 3
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Rajaram, N., Bashtrykov, P., & Jeltsch, A. (2024) · Methods in molecular biology · doi:10.1007/978-1-0716-4051-7_9 · Cited by 3
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Firdaus, A., Izhar, S. K., Yunus, M. H., Khan, Z., & Ansari, M. Y. K. (2025) · CABI biotechnology series. · doi:10.1079/9781800626638.0005 · Cited by 3
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Wu, J., Jang, H., Kwak, H., Son, M., Jiang, W., Hwang, H., Jo, D. H., Kim, D., Kim, S., & Kim, J. H. (2025) · Genome biology · doi:10.1186/s13059-025-03774-5 · Cited by 3
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Apsley, E. J., Riepsaame, J., Cheng, Y., Cowley, S. A., & Becker, E. B. E. (2025) · Disease Models & Mechanisms · doi:10.1242/dmm.052290 · Cited by 3
Glinšek, K., Kramer, L., Krajnc, A., Kranjc, E., Pirher, N., Marušič, J., Hellmann, L., Podobnik, B., Štrukelj, B., Ausländer, D., et al. (2022) · Biotechnology Journal · doi:10.1002/biot.202100499 · Cited by 3
Fischer, J. E., & Glieder, A. (2022) · Methods in molecular biology · doi:10.1007/978-1-0716-2399-2_8 · Cited by 3
Ding, X., Chen, Y., Yang, Z., Wu, H., Cai, Y., Wang, E., Jin, J., & Li, H. (2023) · Applied Microbiology and Biotechnology · doi:10.1007/s00253-023-12383-w · Cited by 3
Zanfrini, E., Bandral, M., Jarc, L., Ramirez-Torres, M. A., Pezzolla, D., Kufrin, V., Rodríguez-Aznar, E., Mojica-Avila, A. K., Cohrs, C. M., Speier, S., et al. (2024) · Scientific Reports · doi:10.1038/s41598-024-69645-4 · Cited by 3
Yamanaka, T., Sogo, A., Maegawa, S., & Kinoshita, M. (2025) · Transgenic Research · doi:10.1007/s11248-025-00434-z · Cited by 3
Bioinformatic tools for CRISPR-mediated genome editing
Gila, F., Shakeri, S., Khoddam, S., Jamali, Z., Sichani, A. S., Dehghan, Z., & Fallahi, J. (2025) · Gene Reports · doi:10.1016/j.genrep.2025.102204 · Cited by 3
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Shrestha, A., Khan, A., & Dey, N. (2019) · Journal of Plant Biochemistry & Physiology · doi:10.4172/2329-9029.1000230 · Cited by 3
Yang, H., Wei, Y., Zhang, Q., Yang, Y., Bi, X., Yang, L., Xiao, N., Zang, A., Ren, L., & Li, X. (2022) · Molecular Medicine Reports · doi:10.3892/mmr.2022.12774 · Cited by 3
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McGraw, C. E., Peng, D., & Sandoval, N. R. (2020) · Current Opinion in Chemical Engineering · doi:10.1016/j.coche.2020.06.003 · Cited by 3
Current trends and recent progress of genetic engineering in genus Phytophthora using CRISPR systems
Javed, M. R., Abbasi, A. Z., Akhtar, M. J., Ghafoor, S., Afzal, M. A., Majeed, Z., & Umer, B. (2021) · Elsevier eBooks · doi:10.1016/b978-0-12-821910-2.00025-4 · Cited by 3
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Anzai, T., Hara, H., Chanthra, N., Sadahiro, T., Ieda, M., Hanazono, Y., & Uosaki, H. (2021) · Methods in molecular biology · doi:10.1007/978-1-0716-1484-6_22 · Cited by 4
Murakami, Y., & Kobayashi, T. (2022) · genesis · doi:10.1002/dvg.23465 · Cited by 3
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Guo, D., Liu, H., Gao, G., Ruzi, A., Wang, K., Wu, H., Lai, K., Liu, Y., Yang, F., Lai, L., et al. (2016) · Stem Cell Research · doi:10.1016/j.scr.2016.11.011 · Cited by 3
Generation of CD16A gene knockout human embryonic stem cell line using CRISPR/Cas9
Wu, S., Deng, H., Lü, B., Yuan, L., & Wang, X. (2022) · Stem Cell Research · doi:10.1016/j.scr.2022.102935 · Cited by 3
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Akhtar, T. (2022) · Pure and Applied Biology · doi:10.19045/bspab.2023.120047 · Cited by 3
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Mathews, B. (2019) · Diva portal (Dalarna University Library) · Cited by 3
Evidence synthesis on the impact of genome editing on plant breeding
Modrzejewski, D. (2020) · eDiss (Georg-August-Universität Göttingen) · doi:10.53846/goediss-8324 · Cited by 3
The Need for Transfer Learning in CRISPR-Cas Off-Target ScoringPreprint
Kota, P. K., Pan, Y., Vu, H.-A., Cao, M., Baraniuk, R. G., & Bao, G. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.08.28.457846 · Cited by 3
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Pan, X., Qu, K., Yuan, H., Xiang, X., Anthon, C., Pashkova, L., Liang, X., Han, P., Corsi, G. I., Xu, F., et al. (2022) · Research Square · doi:10.21203/rs.3.rs-1427273/v1 · Cited by 3
Bouatta, A. M., Lepper, A., & Denninger, P. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.01.11.575165 · Cited by 3
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Raja-Kumar, R.-S., Mesny, F., Basak, A. K., Newfeld, J., Chesneau, G., Entila, F. D., Lee, T. H., Rigerte, L., Acevedo, S. C., Hüettel, B., et al. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.12.01.690973 · Cited by 3
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Wang, S., Feng, Y., Qi, X., Zhou, T., & Liu, J. (2025) · Stem Cell Research · doi:10.1016/j.scr.2025.103721 · Cited by 2
Ryu, S. H., Lee, J., Lee, U., Kim, K., Jun, G.-E., Oh, J., Lee, S., & Chang, S. (2025) · Autophagy · doi:10.1080/15548627.2025.2559689 · Cited by 2
Kapoor, S. A., Choudhary, P., & Kasana, R. C. (2025) · Applied Biochemistry and Biotechnology · doi:10.1007/s12010-025-05382-2 · Cited by 2
Charlier, J., Sherkatghanad, Z., & Makarenkov, V. (2025) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1013606 · Cited by 2
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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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