title: A comprehensive study of RNA secondary structure alignment algorithms.
abstract: RNA secondary structure alignment has received more attention since the discovery of the structure-function relationships in some non-protein-encoding RNAs. However, unlike the pure sequence alignment problem, which has been solved in polynomial time, secondary structure alignment incorporates the base pairings as another information dimension in addition to the base sequence. This problem therefore becomes more challenging. In this study, we classify the selected approaches, and algorithmically illustrate how these methods address the alignment problems with different structure types. Other features such as the types of base pair edit operations supported and the time complexity are also compared.
authors.affiliation: Department of Computer Science and Information Technology, La Trobe University, Melbourne, Victoria, Australia.
authors.forename: Jimmy Ka Ho
authors.initials: JK
authors.lastname: Chiu
authors.affiliation: Department of Computer Science and Information Technology, La Trobe University, Melbourne, Victoria, Australia.
authors.forename: Yi-Ping Phoebe
authors.initials: YP
authors.lastname: Chen
mesh_terms: D000465:Algorithms; D001483:Base Sequence; D009690:Nucleic Acid Conformation; D012313:RNA; D016415:Sequence Alignment; D017423:Sequence Analysis, RNA
chemical_list: D012313:RNA
keywords: RNA alignment; RNA secondary structure alignment; pseudoknot alignment