The DOI matches its Crossref record; 59 of the 59 references it cites were found in a registry or an index.
CRISPRDetect: A flexible algorithm to define CRISPR arrays
Open accessAbstract
BACKGROUND: CRISPR (clustered regularly interspaced short palindromic repeats) RNAs provide the specificity for noncoding RNA-guided adaptive immune defence systems in prokaryotes. CRISPR arrays consist of repeat sequences separated by specific spacer sequences. CRISPR arrays have previously been identified in a large proportion of prokaryotic genomes. However, currently available detection algorithms do not utilise recently discovered features regarding CRISPR loci. RESULTS: We have developed a new approach to automatically detect, predict and interactively refine CRISPR arrays. It is available as a web program and command line from bioanalysis.otago.ac.nz/CRISPRDetect. CRISPRDetect discovers putative arrays, extends the array by detecting additional variant repeats, corrects the direction of arrays, refines the repeat/spacer boundaries, and annotates different types of sequence variations (e.g. insertion/deletion) in near identical repeats. Due to these features, CRISPRDetect has significant advantages when compared to existing identification tools. As well as further support for small medium and large repeats, CRISPRDetect identified a class of arrays with 'extra-large' repeats in bacteria (repeats 44-50 nt). The CRISPRDetect output is integrated with other analysis tools. Notably, the predicted spacers can be directly utilised by CRISPRTarget to predict targets. CONCLUSION: CRISPRDetect enables more accurate detection of arrays and spacers and its gff output is suitable for inclusion in genome annotation pipelines and visualisation. It has been used to analyse all complete bacterial and archaeal reference genomes.
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Clustal W and Clustal X version 2.0
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CRISPR Provides Acquired Resistance Against Viruses in Prokaryotes
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Cpf1 Is a Single RNA-Guided Endonuclease of a Class 2 CRISPR-Cas System
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An updated evolutionary classification of CRISPR–Cas systems
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Evolution and classification of the CRISPR–Cas systems
Makarova, K. S., Haft, D. H., Barrangou, R., Brouns, S. J. J., Charpentier, E., Horvath, P., Moineau, S., Mojica, F. J. M., Wolf, Y. I., Yakunin, A. F., et al. (2011) · Nature Reviews Microbiology · doi:10.1038/nrmicro2577 · Cited by 2,331
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Cited by
Programmed DNA destruction by miniature CRISPR-Cas14 enzymes
Harrington, L. B., Burstein, D., Chen, J. S., Paez-Espino, D., Ma, E., Witte, I. P., Cofsky, J. C., Kyrpides, N. C., Banfield, J. F., & Doudna, J. A. (2018) · Science · doi:10.1126/science.aav4294 · Cited by 1,247
Characterization and Repurposing of Type I and Type II CRISPR–Cas Systems in Bacteria
Hidalgo-Cantabrana, C., Goh, Y. J., & Barrangou, R. (2019) · Journal of Molecular Biology · doi:10.1016/j.jmb.2018.09.013 · Cited by 63
Genome expansion by a CRISPR trimmer-integrase
Wang, J. Y., Tuck, O. T., Skopintsev, P., Soczek, K. M., Li, G., Al-Shayeb, B., Zhou, J., & Doudna, J. A. (2023) · Nature · doi:10.1038/s41586-023-06178-2 · Cited by 33
Mutalik, V. K., & Arkin, A. P. (2022) · iScience · doi:10.1016/j.isci.2022.104121 · Cited by 32
Metadata
- Authors
- Biswas, A., Staals, R. H. J., Morales, S. E., Fineran, P. C., & Brown, C. M.
- Venue
- BMC Genomics
- Published
- 2016-05-17
- Volume
- 17
- Issue
- 1
- Pages
- 356-356
- ISSN
- 1471-2164 (ISSN-L)
- OpenAlex
- W2399809721
- Cited by
- 329
- References
- 59
- FWCI
- 11.59
- Type
- journal article
- Language
- en
- Open access
- gold
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