Identification of 86 candidates for small non-messenger RNAs from the archaeon Archaeoglobus fulgidus, Proc. Natl. Acad. Sci. U.S.A, vol.99, pp.7536-7541, 2002. ,
An updated evolutionary classification of CRISPR-Cas systems, Nat. Rev. Microbiol, vol.13, pp.722-736, 2015. ,
Discovery and functional characterization of diverse class 2 CRISPR-Cas systems, Mol. Cell, vol.60, pp.385-397, 2015. ,
Applications of CRISPR technologies in research and beyond, Nat. Biotechnol, vol.34, pp.933-941, 2016. ,
CRISPR-Cas: biology, mechanisms and relevance, Philos. Trans. R Soc. Lond. B Biol. Sci, vol.371, 2016. ,
DOI : 10.1098/rstb.2015.0496
URL : http://europepmc.org/articles/pmc5052741?pdf=render
Clustered regularly interspaced short palindromic repeats (CRISPRs) for the genotyping of bacterial pathogens, Methods Mol. Biol, vol.551, pp.105-116, 2009. ,
URL : https://hal.archives-ouvertes.fr/hal-00397745
CRISPRFinder: a web tool to identify clustered regularly interspaced short palindromic repeats, Nucleic Acids Res, vol.35, pp.52-57, 2007. ,
URL : https://hal.archives-ouvertes.fr/hal-00194414
CRISPR recognition tool (CRT): a tool for automatic detection of clustered regularly interspaced palindromic repeats, BMC Bioinformatics, vol.8, p.209, 2007. ,
PILER-CR: fast and accurate identification of CRISPR repeats, BMC Bioinformatics, vol.8, p.18, 2007. ,
CRISPRDetect: a flexible algorithm to define CRISPR arrays, BMC Genomics, vol.17, p.356, 2016. ,
CRISPRdigger: detecting CRISPRs with better direct repeat annotations, Sci. Rep, vol.6, p.32942, 2016. ,
CRF: detection of CRISPR arrays using random forest, PeerJ, vol.5, p.3219, 2017. ,
Accurate computational prediction of the transcribed strand of CRISPR non-coding RNAs, Bioinformatics, vol.30, pp.1805-1813, 2014. ,
CRISPRmap: an automated classification of repeat conservation in prokaryotic adaptive immune systems, Nucleic Acids Res, vol.41, pp.8034-8044, 2013. ,
CRISPRstrand: predicting repeat orientations to determine the crRNA-encoding strand at CRISPR loci, Bioinformatics, vol.30, pp.489-496, 2014. ,
Characterizing leader sequences of CRISPR loci, Bioinformatics, vol.32, pp.576-585, 2016. ,
MacSyFinder: a program to mine genomes for molecular systems with an application to CRISPR-Cas systems, PLoS One, vol.9, p.110726, 2014. ,
URL : https://hal.archives-ouvertes.fr/pasteur-01080418
HMMCAS: a web tool for the identification and domain annotations of Cas proteins, IEEE/ACM Trans. Comput. Biol. Bioinform, 2017. ,
Not all predicted CRISPR-Cas systems are equal: isolated cas genes and classes of CRISPR like elements, BMC Bioinformatics, vol.18, p.92, 2017. ,
CRISPRdisco: an automated pipeline for the discovery and analysis of CRISPR-Cas systems, CRISPR J, vol.1, 2018. ,
Replacing suffix trees with enhanced suffix arrays, J. Discrete Algorithms, vol.2, pp.53-86, 2004. ,
CRISPR elements in Yersinia pestis acquire new repeats by preferential uptake of bacteriophage DNA, and provide additional tools for evolutionary studies, Microbiology, vol.151, pp.653-663, 2005. ,
URL : https://hal.archives-ouvertes.fr/hal-01158317
The CRISPRdb database and tools to display CRISPRs and to generate dictionaries of spacers and repeats, BMC Bioinformatics, vol.8, p.172, 2007. ,
URL : https://hal.archives-ouvertes.fr/hal-00194456
The contribution of genetic recombination to CRISPR array evolution, Genome Biol. Evol, vol.7, pp.1925-1939, 2015. ,
Identification of genes that are associated with DNA repeats in prokaryotes, Mol. Microbiol, vol.43, pp.1565-1575, 2002. ,
Prodigal: prokaryotic gene recognition and translation initiation site identification, BMC Bioinformatics, vol.11, p.119, 2010. ,
Diversity, classification and evolution of CRISPR-Cas systems, Curr. Opin. Microbiol, vol.37, pp.67-78, 2017. ,