Unifying evolutionary and thermodynamic information for RNA folding of multiple alignments

Seemann, Stefan E.; Gorodkin, Jan; Backofen, Rolf

The default parameters of PETfold are set by optimizing the MCC of predicted RNA secondary structure to the related Rfam structure annotation over all RNA families in our data set. Hence, we ran PETfold with different values for the single-stranded probability weighting factor ( 0:5) and different reliability thresholds for evolutionary highly conserved single-stranded (p threshold ss ) and base-paired positions (p threshold bp ). The latter two values determine the reliably conserved substructure rel . The conservation part and thermodynamic overlap are equally weighted ( = 1) as PETfold should not be overfitted to RNA families with strong conservation and lower thermodynamic stability or vice versa.