Unifying evolutionary and thermodynamic information for RNA folding of multiple alignments

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

We could not find a general correlation of the best performing reliability thresholds with previously used alignment features such as the structural conservation index (SCI) (23) or mean pairwise sequence identity (MPI). However, structurally diverse alignments tend to benefit from lower reliability thresholds due to a higher evolutionary information content. The alignment diversity can be measured by Pcluster (41) , which divides the sequences of an RNA alignment into subgroups with different consensus structures. On average, PETfold performs best with high-reliability thresholds for RNA families with low number of structural clusters. This correlation is shown in Figure 2 . For instance, the best performing reliability thresholds for Rota_CRE, whose alignment is divided in three clusters by Pcluster, are well described by Figure 2 .