title: Structural alignment of RNA with complex pseudoknot structure.
abstract: The secondary structure of an ncRNA molecule is known to play an important role in its biological functions. Aligning a known ncRNA to a target candidate to determine the sequence and structural similarity helps in identifying de novo ncRNA molecules that are in the same family of the known ncRNA. However, existing algorithms cannot handle complex pseudoknot structures which are found in nature. In this article, we propose algorithms to handle two types of complex pseudoknots: simple non-standard pseudoknots and recursive pseudoknots. Although our methods are not designed for general pseudoknots, it already covers all known ncRNAs in both Rfam and PseudoBase databases. An evaluation of our algorithms shows that it is useful to identify ncRNA molecules in other species which are in the same family of a known ncRNA.
authors.affiliation: Department of Computer Science, University of Hong Kong, Hong Kong.
authors.forename: Thomas K F
authors.initials: TK
authors.lastname: Wong
authors.forename: T W
authors.initials: TW
authors.lastname: Lam
authors.forename: Wing-Kin
authors.initials: WK
authors.lastname: Sung
authors.forename: Brenda W Y
authors.initials: BW
authors.lastname: Cheung
authors.forename: S M
authors.initials: SM
authors.lastname: Yiu
mesh_terms: D000465:Algorithms; D001483:Base Sequence; D003198:Computer Simulation; D006801:Humans; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D022661:RNA, Untranslated / Q000737:chemistry* / Q000145:classification; D016415:Sequence Alignment
chemical_list: D022661:RNA, Untranslated