title: QmRLFS-finder: a model, web server and stand-alone tool for prediction and analysis of R-loop forming sequences.
abstract: 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.
authors.affiliation: Department of Genome and Gene Expression Data Analysis, Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), 30 Biopolis street, #07-01, Singapore 138671.
authors.forename: Piroon
authors.initials: P
authors.lastname: Jenjaroenpun
authors.affiliation: Department of Genome and Gene Expression Data Analysis, Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), 30 Biopolis street, #07-01, Singapore 138671.
authors.forename: Thidathip
authors.initials: T
authors.lastname: Wongsurawat
authors.affiliation: Department of Genome and Gene Expression Data Analysis, Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), 30 Biopolis street, #07-01, Singapore 138671.
authors.forename: Surya Pavan
authors.initials: SP
authors.lastname: Yenamandra
authors.affiliation: Department of Genome and Gene Expression Data Analysis, Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), 30 Biopolis street, #07-01, Singapore 138671 vladimirk@bii.a-star.edu.sg.
authors.forename: Vladimir A
authors.initials: VA
authors.lastname: Kuznetsov
mesh_terms: D000465:Algorithms; D004247:DNA / Q000737:chemistry*; D020407:Internet; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D012313:RNA / Q000737:chemistry*; D017422:Sequence Analysis, DNA / Q000379:methods*; D017423:Sequence Analysis, RNA / Q000379:methods*; D012984:Software
chemical_list: D012313:RNA; D004247:DNA