title: Aligning two RNA secondary structures with l-block.
abstract: RNA sequences can form structures which are conserved throughout evolution and the question of aligning two RNA secondary structures has been extensively studied. Most of the previous alignment algorithms require the input of gap opening and gap extension penalty parameters. The choice of appropriate parameter values is controversial as there is little biological information to guide their assignment. In this paper, we present an algorithm which circumvents this problem. Instead of finding an optimal alignment with predefined gap opening penalty, the algorithm finds the optimal alignment with exact number of aligned blocks.
authors.affiliation: Ontario Cancer Institute, University Health Network, Canada. zwang@uhnres.utoronto.ca
authors.forename: Zhuozhi
authors.initials: Z
authors.lastname: Wang
authors.forename: Elisabeth R M
authors.initials: ER
authors.lastname: Tillier
mesh_terms: D000465:Algorithms; D001483:Base Sequence; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D012313:RNA / Q000737:chemistry* / Q000235:genetics*; D016415:Sequence Alignment / Q000379:methods*; D017423:Sequence Analysis, RNA / Q000379:methods*; D012689:Sequence Homology, Nucleic Acid
chemical_list: D012313:RNA