RNA-Decoder is the first comparative method, which explicitly takes the known protein-coding context of an RNA-sequence alignment into account in order to predict evolutionarily conserved secondary-structure elements, which may span both coding and non-coding regions. On known secondary structures, RNA-Decoder shows a sensitivity similar to the programs Mfold, Pfold and RNAalifold. When scanning the entire genomes of HCV and polio virus for structure elements, RNA-Decoder's results indicate a markedly higher specificity than Mfold, Pfold and RNAalifold