title: Accurate computational prediction of the transcribed strand of CRISPR non-coding RNAs.
abstract: BACKGROUND
  CRISPR RNAs (crRNAs) are a type of small non-coding RNA that form a key part of an acquired immune system in prokaryotes. Specific prediction methods find crRNA-encoding loci in nearly half of sequenced bacterial, and three quarters of archaeal, species. These Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) arrays consist of repeat elements alternating with specific spacers. Generally one strand is transcribed, producing long pre-crRNAs, which are processed to short crRNAs that base pair with invading nucleic acids to facilitate their destruction. No current software for the discovery of CRISPR loci predicts the direction of crRNA transcription.
  
  
  RESULTS
  We have developed an algorithm that accurately predicts the strand of the resulting crRNAs. The method uses as input CRISPR repeat predictions. CRISPRDirection uses parameters that are calculated from the CRISPR repeat predictions and flanking sequences, which are combined by weighted voting. The prediction may use prior coding sequence annotation but this is not required. CRISPRDirection correctly predicted the orientation of 94% of a reference set of arrays.
  
  
  METHODS
  The Perl source code is freely available from http://bioanalysis.otago.ac.nz/CRISPRDirection.
authors.affiliation: Department of Biochemistry, Department of Microbiology and Immunology and Genetics Otago, University of Otago, Dunedin 9054, New Zealand.
authors.forename: Ambarish
authors.initials: A
authors.lastname: Biswas
authors.affiliation: Department of Biochemistry, Department of Microbiology and Immunology and Genetics Otago, University of Otago, Dunedin 9054, New ZealandDepartment of Biochemistry, Department of Microbiology and Immunology and Genetics Otago, University of Otago, Dunedin 9054, New Zealand.
authors.forename: Peter C
authors.initials: PC
authors.lastname: Fineran
authors.affiliation: Department of Biochemistry, Department of Microbiology and Immunology and Genetics Otago, University of Otago, Dunedin 9054, New ZealandDepartment of Biochemistry, Department of Microbiology and Immunology and Genetics Otago, University of Otago, Dunedin 9054, New Zealand.
authors.forename: Chris M
authors.initials: CM
authors.lastname: Brown
mesh_terms: D000465:Algorithms; D001105:Archaea / Q000235:genetics; D064112:Clustered Regularly Interspaced Short Palindromic Repeats; D009690:Nucleic Acid Conformation; D022661:RNA, Untranslated / Q000235:genetics*
chemical_list: D022661:RNA, Untranslated