title: RAGA: RNA sequence alignment by genetic algorithm.
abstract: We describe a new approach for accurately aligning two homologous RNA sequences when the secondary structure of one of them is known. To do so we developed two software packages, called RAGA and PRAGA, which use a genetic algorithm approach to optimize the alignments. RAGA is mainly an extension of SAGA, an earlier package for multiple protein sequence alignment. In PRAGA several genetic algorithms run in parallel and exchange individual solutions. This method allows us to optimize an objective function that describes the quality of a RNA pairwise alignment, taking into account both primary and secondary structure, including pseudoknots. We report results obtained using PRAGA on nine test cases of pairs of eukaryotic small subunit rRNA sequence (nuclear and mitochondrial).
authors.affiliation: EMBL Outstation-The European Bioinformatics Institute, Welcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK. cedric.notredame@ebi.ac.uk
authors.forename: C
authors.initials: C
authors.lastname: Notredame
authors.forename: E A
authors.initials: EA
authors.lastname: O'Brien
authors.forename: D G
authors.initials: DG
authors.lastname: Higgins
mesh_terms: D000465:Algorithms; D000818:Animals; D001483:Base Sequence; D005069:Evaluation Studies as Topic; D006801:Humans; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D012313:RNA / Q000235:genetics*; D000077278:RNA, Mitochondrial; D012335:RNA, Ribosomal / Q000235:genetics*; D016415:Sequence Alignment / Q000379:methods*; D012984:Software
chemical_list: D000077278:RNA, Mitochondrial; D012335:RNA, Ribosomal; D012313:RNA