RNA Consensus Structure Prediction With RNAalifold

Abstract

The secondary structure of most functional RNA molecules is strongly conserved in evolution. Prediction of these conserved structures is therefore of particular interest when studying noncoding RNAs. Moreover, structure predictions on the basis of several sequences produce much more accurate results than energy directed folding of single sequences. The RNAalifold program predicts the consensus structure for a set of aligned sequences taking into account both thermodynamic stability and sequence covariation. In this contribution, we provide a tutorial on how to install and use RNAalifold, as well as a guide on how to interpret the results.