A graphical tool for parametric simulation of the RNA structure formation.
It is known that RNA molecules may fold to suboptimal structures instead of minimum free energy structures due to the kinetics of the folding process and that the kinetic effect becomes more important for large RNA molecules. Thus, prediction of RNA structures can be improved by the study of the RNA folding process. This paper presents a computer program called QFolder, which simulates the RNA folding process in the sense of qualitative kinetics. Given a set of homologous RNA sequences and parameter values, QFolder predicts possible secondary structure motifs and folding events, which might occur during transcription of the RNA molecules. Each predicted structure motif is visualized in graphical form and its certainty factor is computed for evaluation of its prediction. QFolder allows a user to gain insights into the RNA folding process and can be used as useful aids in designing biochemical experiments to elucidate the RNA folding process more accurately.
Han
K
K
Department of Automation Engineering, Inha University, Inchon, Korea. khan@inha.ac.kr
D000465:Algorithms; D001483:Base Sequence; D003198:Computer Simulation; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D012313:RNA / Q000737:chemistry* / Q000378:metabolism; D016415:Sequence Alignment; D012984:Software
D012313:RNA