title: Pure multiple RNA secondary structure alignments: a progressive profile approach.
abstract: In functional, noncoding RNA, structure is often essential to function. While the full 3D structure is very difficult to determine, the 2D structure of an RNA molecule gives good clues to its 3D structure, and for molecules of moderate length, it can be predicted with good reliability. Structure comparison is, in analogy to sequence comparison, the essential technique to infer related function. We provide a method for computing multiple alignments of RNA secondary structures under the tree alignment model, which is suitable to cluster RNA molecules purely on the structural level, i.e., sequence similarity is not required. We give a systematic generalization of the profile alignment method from strings to trees and forests. We introduce a tree profile representation of RNA secondary structure alignments which allows reasonable scoring in structure comparison. Besides the technical aspects, an RNA profile is a useful data structure to represent multiple structures of RNA sequences. Moreover, we propose a visualization of RNA consensus structures that is enriched by the full sequence information.
authors.affiliation: International Graduate School in Bioinformatics and Genome Research, University of Bielefeld, Bielefeld, Germany. mhoechsm@techfak.uni-bielefeld.de
authors.forename: Matthias
authors.initials: M
authors.lastname: Höchsmann
authors.forename: Björn
authors.initials: B
authors.lastname: Voss
authors.forename: Robert
authors.initials: R
authors.lastname: Giegerich
mesh_terms: D020121:5' Untranslated Regions / Q000737:chemistry / Q000235:genetics; D000465:Algorithms; D000818:Animals; D001483:Base Sequence; D019295:Computational Biology / Q000379:methods*; D005293:Ferritins / Q000235:genetics; D006801:Humans; D051379:Mice; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D012313:RNA / Q000737:chemistry* / Q000235:genetics; D012343:RNA, Transfer / Q000737:chemistry / Q000235:genetics; D016415:Sequence Alignment; D012689:Sequence Homology, Nucleic Acid
chemical_list: D020121:5' Untranslated Regions; D012313:RNA; D005293:Ferritins; D012343:RNA, Transfer