R-Loop Tracker: Web Access-Based Tool for R-Loop Detection and Analysis in Genomic DNA Sequences

Brázda, Václav; Havlík, Jan; Kolomazník, Jan; Trenz, Oldřich; Šťastný, Jiří

doi:10.3390/ijms222312857

Open AccessArticle

R-Loop Tracker: Web Access-Based Tool for R-Loop Detection and Analysis in Genomic DNA Sequences

by

Václav Brázda

¹

,

Jan Havlík

²,

Jan Kolomazník

²,

Oldřich Trenz

² and

Jiří Šťastný

^2,3,*

¹

Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic

²

Department of Informatics, Mendel University in Brno, Zemědělská 1, 613 00 Brno, Czech Republic

³

Faculty of Mechanical Engineering, Brno University of Technology, Technická 2896/2, 616 69 Brno, Czech Republic

^*

Author to whom correspondence should be addressed.

Int. J. Mol. Sci. 2021, 22(23), 12857; https://doi.org/10.3390/ijms222312857

Submission received: 29 October 2021 / Revised: 19 November 2021 / Accepted: 25 November 2021 / Published: 27 November 2021

(This article belongs to the Special Issue Bioinformatics of Unusual DNA and RNA Structures)

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Abstract

R-loops are common non-B nucleic acid structures formed by a three-stranded nucleic acid composed of an RNA–DNA hybrid and a displaced single-stranded DNA (ssDNA) loop. Because the aberrant R-loop formation leads to increased mutagenesis, hyper-recombination, rearrangements, and transcription-replication collisions, it is regarded as important in human diseases. Therefore, its prevalence and distribution in genomes are studied intensively. However, in silico tools for R-loop prediction are limited, and therefore, we have developed the R-loop tracker tool, which was implemented as a part of the DNA Analyser web server. This new tool is focused upon (1) prediction of R-loops in genomic DNA without length and sequence limitations; (2) integration of R-loop tracker results with other tools for nucleic acids analyses, including Genome Browser; (3) internal cross-evaluation of in silico results with experimental data, where available; (4) easy export and correlation analyses with other genome features and markers; and (5) enhanced visualization outputs. Our new R-loop tracker tool is freely accessible on the web pages of DNA Analyser tools, and its implementation on the web-based server allows effective analyses not only for DNA segments but also for full chromosomes and genomes.

Keywords: sequence analysis; RNA–DNA hybrid; non-B structure

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MDPI and ACS Style

Brázda, V.; Havlík, J.; Kolomazník, J.; Trenz, O.; Šťastný, J. R-Loop Tracker: Web Access-Based Tool for R-Loop Detection and Analysis in Genomic DNA Sequences. Int. J. Mol. Sci. 2021, 22, 12857. https://doi.org/10.3390/ijms222312857

AMA Style

Brázda V, Havlík J, Kolomazník J, Trenz O, Šťastný J. R-Loop Tracker: Web Access-Based Tool for R-Loop Detection and Analysis in Genomic DNA Sequences. International Journal of Molecular Sciences. 2021; 22(23):12857. https://doi.org/10.3390/ijms222312857

Chicago/Turabian Style

Brázda, Václav, Jan Havlík, Jan Kolomazník, Oldřich Trenz, and Jiří Šťastný. 2021. "R-Loop Tracker: Web Access-Based Tool for R-Loop Detection and Analysis in Genomic DNA Sequences" International Journal of Molecular Sciences 22, no. 23: 12857. https://doi.org/10.3390/ijms222312857

APA Style

Brázda, V., Havlík, J., Kolomazník, J., Trenz, O., & Šťastný, J. (2021). R-Loop Tracker: Web Access-Based Tool for R-Loop Detection and Analysis in Genomic DNA Sequences. International Journal of Molecular Sciences, 22(23), 12857. https://doi.org/10.3390/ijms222312857

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R-Loop Tracker: Web Access-Based Tool for R-Loop Detection and Analysis in Genomic DNA Sequences

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