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Fragments structuraux : comparaison, prédictibilité à partir de la séquence et application à l'identification de protéines de virus

Clovis Galiez 1, 2
Abstract : This thesis investigates the local characterization of protein families at both structural and sequential level. We introduce contact fragments (CF) as parts of protein structure that conciliate spatial locality together with sequential neighborhood. We show that the predictability of CF from the sequence is better than that of contiguous fragments and of structurally distant pairs of fragments. In order to structurally compare CF, we introduce ASD, a novel alignment-free dissimilarity measure that respects triangular inequality while being tolerant to sequence shifts and indels. We show that ASD outperforms classical scores for fragment comparison on practical experiments such that unsupervised classification and structural mining. Ultimately, by integrating the identification of CF from the sequence into a statistical machine learning framework, we developed VIRALpro, a tool that enables the detection of sequences of viral structural proteins.
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Clovis Galiez. Fragments structuraux : comparaison, prédictibilité à partir de la séquence et application à l'identification de protéines de virus. Bio-informatique [q-bio.QM]. Université Rennes 1, 2015. Français. ⟨NNT : 2015REN1S124⟩. ⟨tel-01328182⟩

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