Thermodynamic matchers: strengthening the significance of RNA folding energies.
Thermodynamic RNA secondary structure prediction is an important recipe for the latest generation of functional non-coding RNA finding tools. However, the predicted energy is not strong enough by itself to distinguish a single functional non-coding RNA from other RNA. Here, we analyze how well an RNA molecule folds into a particular structural class with a restricted folding algorithm called Thermodynamic Matcher (TDM). We compare this energy value to that of randomized sequences. We construct and apply TDMs for the non-coding RNA families RNA I and hammerhead ribozyme type III and our results show that using TDMs rather than universal minimum free energy folding allows for highly significant predictions.
Höchsmann
T
T
Faculty of Technology, University Bielefeld, Bielefeld, Germany. thoechsm@techfak.uni-bielefeld.de
Höchsmann
M
M
Giegerich
R
R
D000465:Algorithms; D001483:Base Sequence; D019295:Computational Biology / Q000379:methods*; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D009711:Nucleotides / Q000737:chemistry; D012313:RNA / Q000737:chemistry*; D016337:RNA, Catalytic / Q000737:chemistry; D012984:Software; D013816:Thermodynamics
D009711:Nucleotides; D016337:RNA, Catalytic; C427204:hammerhead ribozyme; D012313:RNA