From consensus structure prediction to RNA gene finding

Reliable structure prediction is a prerequisite for most types of bioinformatical analysis of RNA. Since the accuracy of structure prediction from single sequences is limited, one often resorts to computing the consensus structure for a set of related RNA sequences. Since functionally important RNA structures are expected to evolve much more slowly than the underlying sequences, the pattern of sequence (co-)variation can be exploited to dramatically improve structure prediction. Since a conserved common structure is only expected when the RNA structure is under selective pressure, consensus structure prediction also provides an ideal starting point for the de novo detection of structured non-coding RNAs. Here, we review different strategies for the prediction of consensus secondary structures, and show how these approaches can be used to predict non-coding RNA genes.