CRISPRTarget: bioinformatic prediction and analysis of crRNA targets

RNA Biol. 2013 May;10(5):817-27. doi: 10.4161/rna.24046. Epub 2013 Mar 14.


The bacterial and archaeal CRISPR/Cas adaptive immune system targets specific protospacer nucleotide sequences in invading organisms. This requires base pairing between processed CRISPR RNA and the target protospacer. For type I and II CRISPR/Cas systems, protospacer adjacent motifs (PAM) are essential for target recognition, and for type III, mismatches in the flanking sequences are important in the antiviral response. In this study, we examine the properties of each class of CRISPR. We use this information to provide a tool (CRISPRTarget) that predicts the most likely targets of CRISPR RNAs ( This can be used to discover targets in newly sequenced genomic or metagenomic data. To test its utility, we discover features and targets of well-characterized Streptococcus thermophilus and Sulfolobus solfataricus type II and III CRISPR/Cas systems. Finally, in Pectobacterium species, we identify new CRISPR targets and propose a model of temperate phage exposure and subsequent inhibition by the type I CRISPR/Cas systems.

Keywords: CRISPR; Cas; R-loop; bioinformatics; crRNA; horizontal gene transfer; phage resistance; small RNA targets.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Archaeal Proteins / genetics
  • Archaeal Proteins / metabolism
  • Archaeal Viruses / genetics*
  • Bacteria / genetics*
  • Bacteria / metabolism
  • Bacteria / virology
  • Bacterial Proteins / genetics
  • Bacterial Proteins / metabolism
  • Bacteriophages / genetics*
  • Base Pairing
  • Base Sequence
  • CRISPR-Associated Proteins / genetics*
  • CRISPR-Associated Proteins / metabolism
  • Clustered Regularly Interspaced Short Palindromic Repeats*
  • Computational Biology / methods*
  • DNA, Intergenic / genetics
  • Evolution, Molecular
  • Molecular Sequence Data
  • RNA, Bacterial / genetics
  • Sequence Alignment
  • Streptococcus Phages / genetics
  • Streptococcus thermophilus / genetics
  • Streptococcus thermophilus / virology
  • Sulfolobus solfataricus / genetics
  • Sulfolobus solfataricus / metabolism*


  • Archaeal Proteins
  • Bacterial Proteins
  • CRISPR-Associated Proteins
  • DNA, Intergenic
  • RNA, Bacterial