A METHOD FOR PREDICTING COMMON STRUCTURES OF HOMOLOGOUS RNAS

We have developed a procedure, composed of a set of computer programs, for predicting common RNA structures of homologous sequences. Given a set of homologous RNAs, these programs perform a multiple sequence al ignment, generate a list of possible helical stems that are thermodyna mically favored in RNA folding from a selected individual sequence, es tablish a conserved stem list by inspecting the equivalent base pairin gs and/or conserved helical stems from the derived alignment of homolo gous RNAs, and build common RNA secondary structures with the maximum scores (i.e., compensatory base changes and number of base pairs, etc. ). The approach is a combination of phylogenetic and thermodynamic met hods and has been applied to the prediction of common folding structur es of the 5' untranslated regions in a number of positive RNA viruses. (C) 1995 Academic Press, Inc.