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

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dc.contributor.authorBrázda, Václavcs
dc.contributor.authorHavlík, Jancs
dc.contributor.authorKolomazník, Jancs
dc.contributor.authorTrenz, Oldřichcs
dc.contributor.authorŠťastný, Jiřícs
dc.coverage.issue23cs
dc.coverage.volume22cs
dc.date.issued2021-11-27cs
dc.description.abstractR-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.en
dc.formattextcs
dc.format.extent1-8cs
dc.format.mimetypeapplication/pdfcs
dc.identifier.citationInternational Journal of Molecular Sciences. 2021, vol. 22, issue 23, p. 1-8.en
dc.identifier.doi10.3390/ijms222312857cs
dc.identifier.issn1422-0067cs
dc.identifier.orcid0000-0003-2837-4226cs
dc.identifier.orcid0000-0003-3724-6357cs
dc.identifier.other176636cs
dc.identifier.researcheridF-9582-2011cs
dc.identifier.researcheridF-8025-2012cs
dc.identifier.scopus57191582635cs
dc.identifier.urihttp://hdl.handle.net/11012/204020
dc.language.isoencs
dc.publisherMDPIcs
dc.relation.ispartofInternational Journal of Molecular Sciencescs
dc.relation.urihttps://www.mdpi.com/1422-0067/22/23/12857cs
dc.rightsCreative Commons Attribution 4.0 Internationalcs
dc.rights.accessopenAccesscs
dc.rights.sherpahttp://www.sherpa.ac.uk/romeo/issn/1422-0067/cs
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/cs
dc.subjectsequence analysisen
dc.subjectRNA–DNA hybriden
dc.subjectnon-B structureen
dc.titleR-Loop Tracker: Web Access-Based Tool for R-Loop Detection and Analysis in Genomic DNA Sequencesen
dc.type.driverarticleen
dc.type.statusPeer-revieweden
dc.type.versionpublishedVersionen
sync.item.dbidVAV-176636en
sync.item.dbtypeVAVen
sync.item.insts2025.02.03 15:47:52en
sync.item.modts2025.01.17 19:33:42en
thesis.grantorVysoké učení technické v Brně. Fakulta strojního inženýrství. Ústav automatizace a informatikycs
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