title: Structural RNA alignment by multi-objective optimization.
abstract: BACKGROUND
  The calculation of reliable alignments for structured RNA is still considered as an open problem. One approach is the incorporation of secondary structure information into the optimization criteria by using a weighted sum of sequence and structure components as an objective function. As it is not clear how to choose the weighting parameters, we use multi-objective optimization to calculate a set of Pareto-optimal RNA sequence-structure alignments. The solutions in this set then represent all possible trade-offs between the different objectives, independent of any previous weighting.
  
  
  RESULTS
  We present a practical multi-objective dynamic programming algorithm, which is a new method for the calculation of the set of Pareto-optimal solutions to the pairwise RNA sequence-structure alignment problem. In selected examples, we show the usefulness of this approach, and its advantages over state-of-the-art single-objective algorithms.
  
  
  METHODS
  The source code of our software (ISO C++11) is freely available at http://sysbio.uni-ulm.de/?Software and is licensed under the GNU GPLv3.
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Institute of Theoretical Computer Science, Ulm University, 89069 Ulm, Germany.
authors.forename: Thomas
authors.initials: T
authors.lastname: Schnattinger
authors.forename: Uwe
authors.initials: U
authors.lastname: Schöning
authors.forename: Hans A
authors.initials: HA
authors.lastname: Kestler
mesh_terms: D000465:Algorithms; D009690:Nucleic Acid Conformation; D012313:RNA / Q000737:chemistry*; D012343:RNA, Transfer / Q000737:chemistry; D016415:Sequence Alignment / Q000379:methods*; D017423:Sequence Analysis, RNA / Q000379:methods*; D012984:Software
chemical_list: D012313:RNA; D012343:RNA, Transfer