@Article{Mitrofanov_Ziemann_Alkhnbashi-CRISP_robus_appro-2022,
  author =	 {Mitrofanov, Alexander and Ziemann, Marcus and Alkhnbashi, 
                  Omer S. and Hess, Wolfgang R. and Backofen, Rolf},
  title =	 {{CRISPRtracrRNA}: robust approach for {CRISPR} {tracrRNA} 
                  detection},
  journal =	 {Bioinformatics},
  year =	 {2022},
  volume =	 {38},
  number =	 {Suppl_2},
  pages =	 {ii42-ii48},
  user =	 {backofen},
  pmid =	 {36124799},
  doi = 	 {10.1093/bioinformatics/btac466},
  issn = 	 {1367-4803},
  issn = 	 {1367-4811},
  abstract =	 {MOTIVATION: The CRISPR-Cas9 system is a Type II CRISPR 
                  system that has rapidly become the most versatile and 
                  widespread tool for genome engineering. It consists of two 
                  components, the Cas9 effector protein, and a single guide 
                  RNA that combines the spacer (for identifying the target) 
                  with the tracrRNA, a trans-activating small RNA required for 
                  both crRNA maturation and interference. While there are 
                  well-established methods for screening Cas effector proteins 
                  and CRISPR arrays, the detection of tracrRNA remains the 
                  bottleneck in detecting Class 2 CRISPR systems. RESULTS: We 
                  introduce a new pipeline CRISPRtracrRNA for screening and 
                  evaluation of tracrRNA candidates in genomes. This pipeline 
                  combines evidence from different components of the 
                  Cas9-sgRNA complex. The core is a newly developed structural 
                  model via covariance models from a sequence-structure 
                  alignment of experimentally validated tracrRNAs. As 
                  additional evidence, we determine the terminator signal 
                  (required for the tracrRNA transcription) and the RNA-RNA 
                  interaction between the CRISPR array repeat and the 5'-part 
                  of the tracrRNA. Repeats are detected via an ML-based 
                  approach (CRISPRidenify). Providing further evidence, we 
                  detect the cassette containing the Cas9 (Type II CRISPR 
                  systems) and Cas12 (Type V CRISPR systems) effector protein. 
                  Our tool is the first for detecting tracrRNA for Type V 
                  systems. AVAILABILITY AND IMPLEMENTATION: The implementation 
                  of the CRISPRtracrRNA is available on GitHub upon requesting 
                  the access permission, 
                  (https://github.com/BackofenLab/CRISPRtracrRNA). Data 
                  generated in this study can be obtained upon request to the 
                  corresponding person: Rolf Backofen 
                  (backofen@informatik.uni-freiburg.de). SUPPLEMENTARY 
                  INFORMATION: Supplementary data are available at 
                  Bioinformatics online.}
}