Unifying evolutionary and thermodynamic information for RNA folding of multiple alignments

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

In summary, PETfold's default parameters should be regarded as a reasonable approximation for the RNA family alignments with different levels of diversity. Figure 2 . Correlation between alignment diversity and evolutionary constraint substructures. The correlation between the diversity (number of structural clusters per family calculated by Pcluster) of alignments and the reliability thresholds used by PETfold to predict the best RNA structure, averaged over all families in the data set. We can see that less diverse alignments perform best almost without evolutionary constraints. Intron_gpII (57) is excluded because of its exceedingly high number of 10 structural clusters.