Computational RNA secondary structure design: empirical complexity and improved methods |
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Authors: | Rosalía Aguirre-Hernández Holger H Hoos Anne Condon |
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Institution: | (1) Institute of Applied Mathematics, University of British Columbia, Vancouver, BC V6T 1Z2, Canada;(2) Department of Computer Science, University of British Columbia, Vancouver, BC V6T 1Z4, Canada |
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Abstract: | Background We investigate the empirical complexity of the RNA secondary structure design problem, that is, the scaling of the typical
difficulty of the design task for various classes of RNA structures as the size of the target structure is increased. The
purpose of this work is to understand better the factors that make RNA structures hard to design for existing, high-performance
algorithms. Such understanding provides the basis for improving the performance of one of the best algorithms for this problem,
RNA-SSD, and for characterising its limitations. |
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Keywords: | |
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