Structure predictions for the individual sequences

The consensus structure computed by RNAalifold will contain only pairs that can be formed by most of the sequences. The structures of the individual sequences will typically have additional base pairs that are not part of the consensus structure. Moreover, ncRNA may exhibit a highly conserved core structure while other regions are more variable. It may therefore be desirable to produce structure predictions for one particular sequence, while still using covariance information from other sequences.

This can be accomplished by first computing the consensus structure for all sequences using RNAalifold, then folding individual sequences using RNAfold -C with the consensus structure as a constraint. In constraint folding mode RNAfold -C allows only base pairs to form which are compatible with the constraint structure. This resulting structure typically contains most of the constraint (the consensus structure) plus some additional pairs that are specific for this sequence.