Algorithmes pour l' étude de la structure secondaire des ARN et l'alignement de séquences

Lou Feng 1, 2
2 AMIB - Algorithms and Models for Integrative Biology
LIX - Laboratoire d'informatique de l'École polytechnique [Palaiseau], LRI - Laboratoire de Recherche en Informatique, UP11 - Université Paris-Sud - Paris 11, Inria Saclay - Ile de France
Abstract : This thesis is devoted to the design of algorithms that predict RNA secondary structures and related thermodynamic quantities and sequence alignment algorithms. In the first part, a non-Boltmann Monte-Carlo algorithm is used to estimate energy states density or hybridization energy. Our algorithm to estimate density compares favorably to existing algorithms . Computed denaturation temperature are closer to experimental values than values computed by the two pre-existing algorithms. The second part presents an implementation of dynamic programming algorithms that provides sub-optimal structures where riboswitch functional structures are expected. These predictions compare favorably to the prediction of five other algorithms. Third part is devoted to the search of sub-optimal sequence alignments. For proteins, the focus is given to the improvement of alignment quality, given an identity close to 10-15%. In a comparison with Needman-Wunsch algorithm, entropy computed by our program shows a better correlation with reliable residues positions, according to BAliBASE.
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Lou Feng. Algorithmes pour l' étude de la structure secondaire des ARN et l'alignement de séquences. Bio-informatique [q-bio.QM]. Université Paris Sud - Paris XI, 2012. Français. ⟨tel-00781416⟩

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