title: Secondary structure prediction for aligned RNA sequences.
abstract: Most functional RNA molecules have characteristic secondary structures that are highly conserved in evolution. Here we present a method for computing the consensus structure of a set aligned RNA sequences taking into account both thermodynamic stability and sequence covariation. Comparison with phylogenetic structures of rRNAs shows that a reliability of prediction of more than 80% is achieved for only five related sequences. As an application we show that the Early Noduline mRNA contains significant secondary structure that is supported by sequence covariation.
authors.affiliation: Institut für Theoretische Chemie, Universität Wien, Währingerstrasse 17, Austria.
authors.forename: Ivo L
authors.initials: IL
authors.lastname: Hofacker
authors.forename: Martin
authors.initials: M
authors.lastname: Fekete
authors.forename: Peter F
authors.initials: PF
authors.lastname: Stadler
mesh_terms: D000465:Algorithms; D001105:Archaea / Q000235:genetics; D001483:Base Sequence; D016384:Consensus Sequence / Q000235:genetics; D030561:Databases, Nucleic Acid; D004926:Escherichia coli / Q000235:genetics; D019143:Evolution, Molecular; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D010802:Phylogeny; D011387:Prokaryotic Cells; D012313:RNA / Q000737:chemistry* / Q000235:genetics*; D020871:RNA Stability; D012336:RNA, Ribosomal, 16S / Q000737:chemistry / Q000235:genetics; D012338:RNA, Ribosomal, 23S / Q000737:chemistry / Q000235:genetics; D016415:Sequence Alignment; D012689:Sequence Homology, Nucleic Acid; D013816:Thermodynamics
chemical_list: D012336:RNA, Ribosomal, 16S; D012338:RNA, Ribosomal, 23S; D012313:RNA