title: Detecting conserved secondary structures in RNA molecules using constrained structural alignment.
abstract: Constrained sequence alignment has been studied extensively in the past. Different forms of constraints have been investigated, where a constraint can be a subsequence, a regular expression, or a probability matrix of symbols and positions. However, constrained structural alignment has been investigated to a much lesser extent. In this paper, we present an efficient method for constrained structural alignment and apply the method to detecting conserved secondary structures, or structural motifs, in a set of RNA molecules. The proposed method combines both sequence and structural information of RNAs to find an optimal local alignment between two RNA secondary structures, one of which is a query and the other is a subject structure in the given set. The method allows a biologist to annotate conserved regions, or constraints, in the query RNA structure and incorporates these regions into the alignment process to obtain biologically more meaningful alignment scores. A statistical measure is developed to assess the significance of the scores. Experimental results based on detecting internal ribosome entry sites in the RNA molecules of hepatitis C virus and Trypanosoma brucei demonstrate the effectiveness of the proposed method and its superiority over existing techniques.
authors.affiliation: Bioinformatics Program and Department of Computer Science, New Jersey Institute of Technology, Newark, NJ 07102, USA.
authors.forename: Mugdha
authors.initials: M
authors.lastname: Khaladkar
authors.forename: Vandanaben
authors.initials: V
authors.lastname: Patel
authors.forename: Vivian
authors.initials: V
authors.lastname: Bellofatto
authors.forename: Jeffrey
authors.initials: J
authors.lastname: Wilusz
authors.forename: Jason T L
authors.initials: JT
authors.lastname: Wang
mesh_terms: D000465:Algorithms; D000818:Animals; D001483:Base Sequence; D019295:Computational Biology / Q000379:methods*; D016174:Hepacivirus / Q000235:genetics; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D012313:RNA / Q000737:chemistry* / Q000235:genetics; D014346:Trypanosoma brucei brucei / Q000235:genetics
chemical_list: D012313:RNA