Publication detail

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

BRÁZDA, V. HAVLÍK, J. KOLOMAZNÍK, J. TRENZ, O. ŠŤASTNÝ, J.

Original Title

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

Type

journal article in Web of Science

Language

English

Original 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

Authors

BRÁZDA, V.; HAVLÍK, J.; KOLOMAZNÍK, J.; TRENZ, O.; ŠŤASTNÝ, J.

Released

27. 11. 2021

Publisher

MDPI

ISBN

1422-0067

Periodical

International Journal of Molecular Sciences

Year of study

22

Number

23

State

Swiss Confederation

Pages from

1

Pages to

8

Pages count

8

URL

https://www.mdpi.com/1422-0067/22/23/12857

Full text in the Digital Library

http://hdl.handle.net/11012/204020

BibTex

@article{BUT176636,
  author="Václav {Brázda} and Jan {Havlík} and Jan {Kolomazník} and Oldřich {Trenz} and Jiří {Šťastný}",
  title="R-Loop Tracker: Web Access-Based Tool for R-Loop Detection and Analysis in Genomic DNA Sequences",
  journal="International Journal of Molecular Sciences",
  year="2021",
  volume="22",
  number="23",
  pages="1--8",
  doi="10.3390/ijms222312857",
  issn="1422-0067",
  url="https://www.mdpi.com/1422-0067/22/23/12857"
}