title: Toward assigning helical regions in alignments of ribosomal RNA and testing the appropriateness of evolutionary models.
abstract: We suggest a nucleotide substitution model that takes correlation between base-paired nucleotides into account. The model includes the estimation of the transition-transversion ratio and allows inference of the shape parameter of a discrete gamma distribution to include rate heterogeneity. A Cox-test statistic, applied to a diatom ribosomal RNA alignment, shows that the suggested correlation model explains evolution of the stem region better than usual independence models. Moreover, the Cox-test procedure is extended to shed some light upon the problem of assigning helical regions in a secondary structure based alignment. This approach provides an estimate of the percentage of stem positions that do not appear to be correlated.
authors.affiliation: Theoretische Chemie, Technische Universität München, Lichtenbergstr. 4, D-85747 Garching, Germany. schoeniger@theochem.tu-muenchen.de
authors.forename: M
authors.initials: M
authors.lastname: Schöniger
authors.forename: A
authors.initials: A
authors.lastname: von Haeseler
mesh_terms: D001483:Base Sequence; D017377:Diatoms / Q000235:genetics; D019143:Evolution, Molecular; D008957:Models, Genetic; D009010:Monte Carlo Method; D009690:Nucleic Acid Conformation; D010802:Phylogeny; D016016:Proportional Hazards Models; D012335:RNA, Ribosomal / Q000737:chemistry* / Q000235:genetics*; D016415:Sequence Alignment
chemical_list: D012335:RNA, Ribosomal