title: Using multiple alignments and phylogenetic trees to detect RNA secondary structure.
abstract: We describe a statistical method to determine if a pair of columns in a multiple alignment of a homologous family of RNA sequences shows evidence of being base paired. The method makes explicit use of a given phylogenetic tree for the sequences in the alignment. It is tested on a multiple alignment of 16S rRNA sequences with good results.
authors.affiliation: Department of Computer Engineering, Lepton Incorporated, University of California at Santa Cruz, USA. bgulko@LeptonCorp.com
authors.forename: B
authors.initials: B
authors.lastname: Gulko
authors.forename: D
authors.initials: D
authors.lastname: Haussler
mesh_terms: D001482:Base Composition; D001483:Base Sequence; D003198:Computer Simulation; D019143:Evolution, Molecular; D008957:Models, Genetic; D009690:Nucleic Acid Conformation; D010802:Phylogeny; D011336:Probability; D012313:RNA / Q000737:chemistry* / Q000235:genetics*; D012336:RNA, Ribosomal, 16S / Q000737:chemistry* / Q000235:genetics; D015203:Reproducibility of Results; D016415:Sequence Alignment
chemical_list: D012336:RNA, Ribosomal, 16S; D012313:RNA