QmRLFS-finder: a model, web server and stand-alone tool for prediction and analysis of R-loop forming sequences

The possible formation of three-stranded RNA and DNA hybrid structures (R-loops) in thousands of functionally important guanine-rich genic and inter-genic regions could suggest their involvement in transcriptional regulation and even development of diseases. Here, we introduce the first freely avail...

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Main Authors:	Jenjaroenpun, Piroon, Wongsurawat, Thidathip, Yenamandra, Surya Pavan, Kuznetsov, Vladimir A.
Format:	Online
Language:	English
Published:	Oxford University Press 2015
Online Access:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4489302/

id	pubmed-4489302
recordtype	oai_dc
spelling	pubmed-44893022015-07-07 QmRLFS-finder: a model, web server and stand-alone tool for prediction and analysis of R-loop forming sequences Jenjaroenpun, Piroon Wongsurawat, Thidathip Yenamandra, Surya Pavan Kuznetsov, Vladimir A. Web Server issue The possible formation of three-stranded RNA and DNA hybrid structures (R-loops) in thousands of functionally important guanine-rich genic and inter-genic regions could suggest their involvement in transcriptional regulation and even development of diseases. Here, we introduce the first freely available R-loop prediction program called Quantitative Model of R-loop Forming Sequence (RLFS) finder (QmRLFS-finder), which predicts RLFSs in nucleic acid sequences based on experimentally supported structural models of RLFSs. QmRLFS-finder operates via a web server or a stand-alone command line tool. This tool identifies and visualizes RLFS coordinates from any natural or artificial DNA or RNA input sequences and creates standards-compliant output files for further annotation and analysis. QmRLFS-finder demonstrates highly accurate predictions of the detected RLFSs, proposing new perspective to further discoveries in R-loop biology, biotechnology and molecular therapy. QmRLFS-finder is freely available at http://rloop.bii.a-star.edu.sg/?pg=qmrlfs-finder. Oxford University Press 2015-07-01 2015-04-16 /pmc/articles/PMC4489302/ /pubmed/25883153 http://dx.doi.org/10.1093/nar/gkv344 Text en © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research. http://creativecommons.org/licenses/by/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
repository_type	Open Access Journal
institution_category	Foreign Institution
institution	US National Center for Biotechnology Information
building	NCBI PubMed
collection	Online Access
language	English
format	Online
author	Jenjaroenpun, Piroon Wongsurawat, Thidathip Yenamandra, Surya Pavan Kuznetsov, Vladimir A.
spellingShingle	Jenjaroenpun, Piroon Wongsurawat, Thidathip Yenamandra, Surya Pavan Kuznetsov, Vladimir A. QmRLFS-finder: a model, web server and stand-alone tool for prediction and analysis of R-loop forming sequences
author_facet	Jenjaroenpun, Piroon Wongsurawat, Thidathip Yenamandra, Surya Pavan Kuznetsov, Vladimir A.
author_sort	Jenjaroenpun, Piroon
title	QmRLFS-finder: a model, web server and stand-alone tool for prediction and analysis of R-loop forming sequences
title_short	QmRLFS-finder: a model, web server and stand-alone tool for prediction and analysis of R-loop forming sequences
title_full	QmRLFS-finder: a model, web server and stand-alone tool for prediction and analysis of R-loop forming sequences
title_fullStr	QmRLFS-finder: a model, web server and stand-alone tool for prediction and analysis of R-loop forming sequences
title_full_unstemmed	QmRLFS-finder: a model, web server and stand-alone tool for prediction and analysis of R-loop forming sequences
title_sort	qmrlfs-finder: a model, web server and stand-alone tool for prediction and analysis of r-loop forming sequences
description	The possible formation of three-stranded RNA and DNA hybrid structures (R-loops) in thousands of functionally important guanine-rich genic and inter-genic regions could suggest their involvement in transcriptional regulation and even development of diseases. Here, we introduce the first freely available R-loop prediction program called Quantitative Model of R-loop Forming Sequence (RLFS) finder (QmRLFS-finder), which predicts RLFSs in nucleic acid sequences based on experimentally supported structural models of RLFSs. QmRLFS-finder operates via a web server or a stand-alone command line tool. This tool identifies and visualizes RLFS coordinates from any natural or artificial DNA or RNA input sequences and creates standards-compliant output files for further annotation and analysis. QmRLFS-finder demonstrates highly accurate predictions of the detected RLFSs, proposing new perspective to further discoveries in R-loop biology, biotechnology and molecular therapy. QmRLFS-finder is freely available at http://rloop.bii.a-star.edu.sg/?pg=qmrlfs-finder.
publisher	Oxford University Press
publishDate	2015
url	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4489302/
_version_	1613243125203992576

QmRLFS-finder: a model, web server and stand-alone tool for prediction and analysis of R-loop forming sequences

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