AUTOMATIC DETECTION OF CONSERVED RNA STRUCTURE ELEMENTS IN COMPLETE RNA VIRUS GENOMES

We propose a new method for detecting conserved RNA secondary structur es in a family of related RNA sequences. Our method is based on a comb ination of thermodynamic structure prediction and phylogenetic compari son. In contrast to purely phylogenetic methods, our algorithm can be used for small data sets of similar to 10 sequences, efficiently explo iting the information contained in the sequence variability. The proce dure constructs a prediction only for those parts of sequences that ar e consistent with a single conserved structure. Our implementation pro duces reasonable consensus structures without user interference. As an example we have analysed the complete HIV-1 and hepatitis C virus (HC V) genomes as well as the small segment of hantavirus. Our method conf irms the known structures in HIV-1 and predicts previously unknown con served RNA secondary structures in HCV.