@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},
doi = {10.1093/bioinformatics/btac466},
volume = {38},
user = {backofen},
pmid = {36124799},
pages = {ii42-ii48},
number = {Suppl_2},
issn = {1367-4803},
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.}
}