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

Nucleic Acids Res. 2015 Jul 1;43(W1):W527-34. doi: 10.1093/nar/gkv344. Epub 2015 Apr 16.


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.

Publication types

  • Research Support, Non-U.S. Gov't
  • Validation Study

MeSH terms

  • Algorithms
  • DNA / chemistry*
  • Internet
  • Models, Molecular
  • Nucleic Acid Conformation
  • RNA / chemistry*
  • Sequence Analysis, DNA / methods*
  • Sequence Analysis, RNA / methods*
  • Software*


  • RNA
  • DNA