title: RNA-Pareto: interactive analysis of Pareto-optimal RNA sequence-structure alignments.
abstract: Incorporating secondary structure information into the alignment process improves the quality of RNA sequence alignments. Instead of using fixed weighting parameters, sequence and structure components can be treated as different objectives and optimized simultaneously. The result is not a single, but a Pareto-set of equally optimal solutions, which all represent different possible weighting parameters. We now provide the interactive graphical software tool RNA-Pareto, which allows a direct inspection of all feasible results to the pairwise RNA sequence-structure alignment problem and greatly facilitates the exploration of the optimal solution set.
authors.affiliation: Institute of Theoretical Computer Science, Medical Systems Biology and Biology II, Ulm University, D-89069 Ulm, Germany.
authors.forename: Thomas
authors.initials: T
authors.lastname: Schnattinger
authors.forename: Uwe
authors.initials: U
authors.lastname: Schöning
authors.forename: Anita
authors.initials: A
authors.lastname: Marchfelder
authors.forename: Hans A
authors.initials: HA
authors.lastname: Kestler
mesh_terms: D000465:Algorithms; D001483:Base Sequence; D019295:Computational Biology / Q000379:methods*; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D012313:RNA / Q000737:chemistry*; D016415:Sequence Alignment / Q000379:methods*; D017423:Sequence Analysis, RNA / Q000379:methods*; D012689:Sequence Homology, Nucleic Acid; D012984:Software
chemical_list: D012313:RNA