An RNA folding method capable of identifying pseudoknots and base triples

MOTIVATION: Recently, we described a Maximum Weighted Matching (MWM) methodfor RNA structure prediction. The MWM method is capable of detectingpseudoknots and other tertiary base-pairing interactions in acomputationally efficient manner (Cary and Stormo, Proceedings of the ThirdInternational Conference on Intelligent Systems for Molecular Biology, pp.75-80, 1995). Here we report on the results of our efforts to improve theMWM method's predictive accuracy, and show how the method can be extendedto detect base interactions formerly inaccessible to automated RNA modelingtechniques. RESULTS: Improved performance in MWM structure prediction wasachieved in two ways. First, new ways of calculating base pair likelihoodshave been developed. These allow experimental data and combined statisticaland thermodynamic information to be used by the program. Second, accuracywas improved by developing techniques for filtering out spurious base pairspredicted by the MWM program. We also demonstrate here a means by which theMWM folding method may be used to detect the presence of base triples inRNAs. AVAILABILITY: http://www.cshl.org/mzhanglab/tabaska/j axpage. htmlCONTACT: tabaska@cshl.org