%0 Journal Article %T Efficient sampling of RNA secondary structures from the Boltzmann ensemble of low-energy: The boustrophedon method %+ Algorithms and Models for Integrative Biology (AMIB ) %+ Laboratoire d'informatique de l'École polytechnique [Palaiseau] (LIX) %A Ponty, Yann %< avec comité de lecture %@ 0303-6812 %J Journal of Mathematical Biology %I Springer Verlag (Germany) %V 56 %N 1-2 %P 107--127 %8 2008 %D 2008 %R 10.1007/s00285-007-0137-z %Z Computer Science [cs]/Bioinformatics [q-bio.QM] %Z Life Sciences [q-bio]/Quantitative Methods [q-bio.QM]Journal articles %X We adapt here a surprising technique, the boustrophedon method, to speed up the sampling of RNA secondary structures from the Boltzmann low-energy ensemble. This technique is simple and its implementation straight-forward, as it only requires a permutation in the order of some operations already performed in the stochastic traceback stage of these algorithms. It nevertheless greatly improves their worst-case complexity from O(n^2) to O(n log(n)), for n the size of the original sequence. Moreover the average-case complexity of the generation is shown to be improved from O(n√n) to O(n log(n)) in an Boltzmann-weighted homopolymer model based on the Nussinov–Jacobson free-energy model. These results are extended to the more realistic Turner free-energy model through experiments performed on both structured (Drosophilia melanogaster mRNA 5S) and hybrid (Staphylococcus aureus RNAIII) RNA sequences, using a boustrophedon modified version of the popular software UnaFold. This improvement allows for the sampling of greater and more significant sets of structures in a given time. %G English %L inria-00548863 %U https://inria.hal.science/inria-00548863 %~ X %~ EC-PARIS %~ CNRS %~ INRIA %~ UNIV-PSUD %~ LIX %~ INRIA-SACLAY %~ X-LIX %~ X-DEP %~ X-DEP-INFO %~ INRIA_TEST %~ TESTALAIN1 %~ UMR8623 %~ INRIA2 %~ UNIV-PARIS-SACLAY %~ UNIV-PSUD-SACLAY