Martin Fekete, Ivo Hofacker, Peter Stadler

Paper #: 01-11-067

Most functional RNA molecules have characteristic secondary structures that are highly conserved in evolution. Here we present a method for computing the consensus structure of a set of aligned RNA sequences taking into account both thermodynamic stability and sequence covariation. Comparison with phylogenetic structures of rRNAs shows that a reliability of prediction of more than 80% is achieved for only five related sequences. As an application we show that the Early Noduline mRNA contains significant secondary structure that is supported by sequence covariation.