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Updated: May 7, 2026

RNA Secondary Structure Prediction Using High-throughput SHAPE
Published on: May 31, 2013
RNA-Pareto: interactive analysis of Pareto-optimal RNA sequence-structure alignments
Thomas Schnattinger1, Uwe Schöning, Anita Marchfelder
1Institute of Theoretical Computer Science, Medical Systems Biology and Biology II, Ulm University, D-89069 Ulm, Germany.
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.
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