title: PILER-CR: fast and accurate identification of CRISPR repeats.
abstract: 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.
  
  
  CONCLUSIONS
  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.
authors.affiliation: bob@drive5.com
authors.forename: Robert C
authors.initials: RC
authors.lastname: Edgar
mesh_terms: D000465:Algorithms; D001105:Archaea / Q000235:genetics*; D001419:Bacteria / Q000235:genetics*; D017124:Conserved Sequence; D019641:DNA, Archaeal; D004269:DNA, Bacterial; D023281:Genomics; D016247:Information Storage and Retrieval; D012091:Repetitive Sequences, Nucleic Acid; D012680:Sensitivity and Specificity; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software
chemical_list: D019641:DNA, Archaeal; D004269:DNA, Bacterial