Automatic Detection of Conserved RNA Structure Elements in Complete RNA Virus Genomes

We propose a new method for detecting conserved RNA secondary structures in a family of related RNA sequences. Our method is based on a combination of thermodynamic structure prediction and phylogenetic comparison. In contrast to purely phylogenetic methods, our algorithm can be used for small data sets of about 10 sequences, efficiently exploiting the information contained in the sequence variability. The procedure constructs a prediction only for those parts of sequences that are consistent with a single conserved structure. Our implementation produces reasonable consensus structures without user interference. As an example we have analyzed complete HIV-1 and Hepatitis C virus genomes as well as the small segment of Hanta virus. Our method confirms the known structures in HIV-I and predicts previously unknown conserved RNA secondary structures in HCV.