title: Prediction of RNA base pairing probabilities on massively parallel computers.
abstract: We present an implementation of McCaskill's algorithm for computing the base pair probabilities of an RNA molecule for massively parallel message passing architectures. The program can be used to routinely fold RNA sequences of more than 10,000 nucleotides. Applications to complete viral genomes are discussed.
authors.affiliation: Institut für Theoretische Chemie, Universität Wien, Austria.
authors.forename: M
authors.initials: M
authors.lastname: Fekete
authors.forename: I L
authors.initials: IL
authors.lastname: Hofacker
authors.forename: P F
authors.initials: PF
authors.lastname: Stadler
mesh_terms: D000465:Algorithms; D020029:Base Pairing; D001483:Base Sequence; D001699:Biometry; D003201:Computers; D015497:HIV-1 / Q000235:genetics; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D012313:RNA / Q000737:chemistry* / Q000235:genetics*; D012367:RNA, Viral / Q000737:chemistry / Q000235:genetics; D017423:Sequence Analysis, RNA / Q000706:statistics & numerical data*
chemical_list: D012367:RNA, Viral; D012313:RNA