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Algorithmes pour la recherche de classes de gènes en relations fonctionnelles par analyse de proximités et de similarités de séquences

Abstract : Our study focuses on ABC transporters in complete bacterial genomes. The bioinformatic analysis of these systems includes the identification of partners, the assembly, the reconstruction of incomplete systems, the classification in sub-families, and the identification of the carried substrate. This thesis proposes tools allowing the study of these problems by using computational methods. The biological hypotheses employed are : (i) neighbor genes on the chromosome can be implicated in a same metabolic process if they are conserved during evolution, and (ii) genes with similarities of sequences can allow the synthesis of proteins of the same function. Three studies have been made on ABC transporters : * The exploration of chromosomical neighborhood. According to the hypothesis which says that the closer the genes conserved in the neighborhood of a transporter are, the stronger their functionnal link with the transporter is, we try to identify the carried substrate or associations between genes. This problem is treated by a resolution method stemming from the constraints satisfaction problems. * Classification. ABC transporters are classified into big categories in function of the molecules they carry (sugars, ...). For each domain, by representing the homological relations by a graph, the research for the high density areas allow us to determine sub-classes of substrate. * The reconstitution of incomplete systems. ABC transporters are assembled using the chromosomical proximity of the genes coding for the domains, and the compatibility of the sub-families of the domains. When the proximity is not respected, we use a strategy developped from a method of graph analysis to assemble the domains and predict the active systems. These methods, complementary to the identification of partners and of the assembly process, allow a functional study of the ABC transporters. They could be applied to other biological systems.
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https://tel.archives-ouvertes.fr/tel-00008447
Contributor : Tristan Colombo <>
Submitted on : Friday, February 11, 2005 - 10:31:10 AM
Last modification on : Thursday, January 18, 2018 - 1:38:11 AM
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Tristan Colombo. Algorithmes pour la recherche de classes de gènes en relations fonctionnelles par analyse de proximités et de similarités de séquences. Autre [cs.OH]. Université de la Méditerranée - Aix-Marseille II, 2004. Français. ⟨tel-00008447⟩

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