title: Prediction of common secondary structures of RNAs: a genetic algorithm approach.
abstract: In this study we apply a genetic algorithm to a set of RNA sequences to find common RNA secondary structures. Our method is a three-step procedure. At the first stage of the procedure for each sequence, a genetic algorithm is used to optimize the structures in a population to a certain degree of stability. In this step, the free energy of a structure is the fitness criterion for the algorithm. Next, for each structure, we define a measure of structural conservation with respect to those in other sequences. We use this measure in a genetic algorithm to improve the structural similarity among sequences for the structures in the population of a sequence. Finally, we select those structures satisfying certain conditions of structural stability and similarity as predicted common structures for a set of RNA sequences. We have obtained satisfactory results from a set of tRNA, 5S rRNA, rev response elements (RRE) of HIV-1 and RRE of HIV-2/SIV, respectively.
authors.affiliation: Advanced Biomedical Computing Center, SAIC, NCI/FCRDC, Frederick, MD 21702, USA. chen@ncifcrf.gov
authors.forename: J H
authors.initials: JH
authors.lastname: Chen
authors.forename: S Y
authors.initials: SY
authors.lastname: Le
authors.forename: J V
authors.initials: JV
authors.lastname: Maizel
mesh_terms: D000465:Algorithms; D001483:Base Sequence; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D012313:RNA / Q000737:chemistry* / Q000235:genetics; D012689:Sequence Homology, Nucleic Acid
chemical_list: D012313:RNA