Comparison of RNA secondary structure prediction methods with PARS data. For each RNA, the reference secondary structure, the RNAstructure MFE prediction, the “sample and select” prediction with PARS, and the SeqFold prediction with PARS are shown. (A) The P9-9.2 domain of the Tetrahymena ribozyme (Guo et al. 2004). (B) The E1 domain of the ASH1 mRNA (Chartrand et al. 2002). (C) The noncoding RNA SNR10. In the case that the “sample and select” algorithm outputs alternative structure models, the one most matching the reference structures is presented. For each predicted secondary structure, the red bases correspond to errors compared to the reference structures.
