The DOI matches its Crossref record; 15 of the 15 references it cites were found in a registry or an index.
PILER-CR: Fast and accurate identification of CRISPR repeats
Open accessAbstract
BACKGROUND: Sequencing of prokaryotic genomes has recently revealed the presence of CRISPR elements: short, highly conserved repeats separated by unique sequences of similar length. The distinctive sequence signature of CRISPR repeats can be found using general-purpose repeat- or pattern-finding software tools. However, the output of such tools is not always ideal for studying these repeats, and significant effort is sometimes needed to build additional tools and perform manual analysis of the output. RESULTS: We present PILER-CR, a program specifically designed for the identification and analysis of CRISPR repeats. The program executes rapidly, completing a 5 Mb genome in around 5 seconds on a current desktop computer. We validate the algorithm by manual curation and by comparison with published surveys of these repeats, finding that PILER-CR has both high sensitivity and high specificity. We also present a catalogue of putative CRISPR repeats identified in a comprehensive analysis of 346 prokaryotic genomes. CONCLUSION: PILER-CR is a useful tool for rapid identification and classification of CRISPR repeats. The software is donated to the public domain. Source code and a Linux binary are freely available at http://www.drive5.com/pilercr.
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Cites
MUSCLE: multiple sequence alignment with high accuracy and high throughput
Edgar, R. C. (2004) · Nucleic Acids Research · doi:10.1093/nar/gkh340 · Cited by 44,662
Self-citationMUSCLE: a multiple sequence alignment method with reduced time and space complexity
Edgar, R. C. (2004) · BMC Bioinformatics · doi:10.1186/1471-2105-5-113 · Cited by 8,970
Self-citationComplete Genome Sequence of the Methanogenic Archaeon, Methanococcus jannaschii
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Identification of genes that are associated with DNA repeats in prokaryotes
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PILER: identification and classification of genomic repeats
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Cited by
Cpf1 Is a Single RNA-Guided Endonuclease of a Class 2 CRISPR-Cas System
Zetsche, B., Gootenberg, J. S., Abudayyeh, O. O., Slaymaker, I. M., Makarova, K. S., Essletzbichler, P., Volz, S. E., Joung, J., van der Oost, J., Regev, A., et al. (2015) · Cell · doi:10.1016/j.cell.2015.09.038 · Cited by 4,761
CRISPRFinder: a web tool to identify clustered regularly interspaced short palindromic repeats
Grissa, I., Vergnaud, G., & Pourcel, C. (2007) · Nucleic Acids Research · doi:10.1093/nar/gkm360 · Cited by 1,875
RNA-guided genetic silencing systems in bacteria and archaea
Wiedenheft, B., Sternberg, S. H., & Doudna, J. A. (2012) · Nature · doi:10.1038/nature10886 · Cited by 1,851
Schwengers, O., Jelonek, L., Dieckmann, M. A., Beyvers, S., Blom, J., & Goesmann, A. (2021) · Microbial Genomics · doi:10.1099/mgen.0.000685 · Cited by 1,424
Transcriptome Engineering with RNA-Targeting Type VI-D CRISPR Effectors
Konermann, S., Lotfy, P., Brideau, N. J., Oki, J., Shokhirev, M. N., & Hsu, P. D. (2018) · Cell · doi:10.1016/j.cell.2018.02.033 · Cited by 1,164
Metadata
- Authors
- Edgar, R. C.
- Venue
- BMC Bioinformatics
- Published
- 2007-01-20
- Volume
- 8
- Issue
- 1
- Pages
- 18-18
- ISSN
- 1471-2105 (ISSN-L)
- OpenAlex
- W2134023754
- Cited by
- 377
- References
- 15
- FWCI
- 3.11
- Type
- journal article
- Language
- en
- Open access
- gold
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