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Reconstruction ab initio de voies métaboliques - Formalisation et approches combinatoires

Frédéric Boyer 1, 2
2 HELIX - Computer science and genomics
Inria Grenoble - Rhône-Alpes, LBBE - Laboratoire de Biométrie et Biologie Evolutive - UMR 5558
Abstract : Reconstructing the metabolic pathways of an organism is a task of major importance and several approaches have already been proposed in order to help biologists in this task but more exploratory approaches are needed.

The first part of this thesis emphasis on what we call ab initio metabolic pathway reconstruction. This consists in finding inside the global network of chemical reactions occurring in a living organism, a sub network connecting at least two chemical compounds. Given a set of biochemical reactions together with their substrates and products, we consider the reactions as transfers of atoms between the chemical compounds and we look for sequences of reactions transferring a maximal (or preset) number of atoms between a source and a sink compound. We state this problem as the one of finding a composition of partial injections that maximises the image size. The theoretical complexity of this problem has been studied and a practical algorithm to solve it is presented.

The second part presents a formalization of a problem concerning graphs comparison. The particular case treated in this thesis concerns the comparison of a network of reactions with the spatial organization of genes on the genome. This comparison permits to identify operon encoded metabolic pathways.
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Submitted on : Monday, August 23, 2004 - 12:36:26 PM
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Frédéric Boyer. Reconstruction ab initio de voies métaboliques - Formalisation et approches combinatoires. Autre [cs.OH]. Université Joseph-Fourier - Grenoble I, 2004. Français. ⟨tel-00006728⟩

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