PILER-CR: Fast and accurate identification of CRISPR repeats

By Robert C. Edgar. BMC Bioinformatics, 2007

377 citations recorded by the source corpus.

BackgroundSequencing 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.ResultsWe 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.ConclusionPILER-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.

Subfields: Cellular and Molecular Neuroscience, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/f3a71325320b541eeaab5e7b54ee218258630fe8

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In Cellular and Molecular Neuroscience

In Molecular Biology

Citations in the corpus

The standard operating procedure of the DOE-JGI Microbial Genome Annotation Pipeline (MGAP v.4) (2015, neutral): “06 [5].”
CRISPRDetect: A flexible algorithm to define CRISPR arrays (2016, methodology): “Then, to facilitate CRISPR prediction and analysis, a number of tools were developed, including both command-line executable programs (e.g. CRT [13], MINCED [14] and PILER-CR [15]) and web-applications (e.g. CRISPRFinder, CRISPI) [16, 17].”
Transcriptome engineering with RNA-targeting Type VI-D CRISPR effectors (2018, positive): “…CRISPR array as a search anchor, we first obtained all prokaryotic genome assemblies and scaffolds from the NCBIWGSdatabase and adapted algorithms for de novo CRISPR array detection (Bland et al., 2007; Edgar, 2007; Grissa et al., 2007) to identify 21,175 putative CRISPR repeat arrays (Figure S1A).”
Cpf1 is a single RNA-guided endonuclease of a class 2 CRISPR-Cas system. (2015, positive): “CRISPR repeats were identified using PILER-CR (Edgar, 2007) and CRISPRfinder (Grissa et al.”
The human gut virome is highly diverse, stable and individual-specific (2019, background): “06 (Edgar, 2007).”
Bakta: rapid and standardized annotation of bacterial genomes via alignment-free sequence identification (2021, positive): “CRISPR arrays are predicted by Piler-CR [22].”
Discovery and functional characterization of diverse Class 2 CRISPR-Cas systems (2015, methodology): “CRISPR repeats were identified using PILER-CR (Edgar, 2007) or, for degenerate repeats, CRISPRfinder (Grissa et al., 2007).”
CRISPRCasFinder, an update of CRISRFinder, includes a portable version, enhanced performance and integrates search for Cas proteins (2018, background): “Predictions were compared to the expert-curated annotations in CRISPRdb (used as a reference-set) and to three CRISPR detection programs PILER-CR, CRT and CRISPRDetect.”
iPHoP: An integrated machine learning framework to maximize host prediction for metagenome-derived viruses of archaea and bacteria (2023, positive): “Finally, for CRISPR-based predictions, CRISPR spacers were predicted de novo in all 121,781 genomes (i.e., representatives, clustered, and duplicates), with CRT 1.2 [60] and PilerCR [61] using custom python scripts from https://github.com/snayfach/MGV/tree/master/crispr_ spacers [33].”
RNA-guided genetic silencing systems in bacteria and archaea (2012, background): “The sequence diversity of these repetitive loci initially limited their detection and obscured their relationship, but computational methods have been developed for detecting repeat patterns rather than related sequence”
MacSyFinder: A Program to Mine Genomes for Molecular Systems with an Application to CRISPR-Cas Systems (2014, background): “Tools are available to detect and analyse CRISPR arrays [17–19], however, no program is available to detect and class cas operons themselves.”
CRISPRFinder: a web tool to identify clustered regularly interspaced short palindromic repeats (2007, methodology): “Recently, two CRISPR- dedicated software tools were proposed, CRT (http://www.room220.com/crt) and PILER-CR ( 25 ).”