Alignements locaux pour la reconnaissance de repliements des protéines par programmation linéaire en nombres entiers

Guillaume Collet 1
1 SYMBIOSE - Biological systems and models, bioinformatics and sequences
IRISA - Institut de Recherche en Informatique et Systèmes Aléatoires, Inria Rennes – Bretagne Atlantique
Abstract : Detecting similarities and homologies between proteins is a key step during the annotation process. To find such homologies, multiple sequence alignments are widely used. These methods provide global to local alignment features. Nevertheless, in the so called "Twilight Zone", one must relies on fold recognition methods to find homologous proteins. In this field, the Protein Threading Problem (PTP) uses pairwise parameters to globaly align a protein sequence with a protein structure. As far as we know, no local alignment method using pairwise parameters exists. Based on the PTP, we proposed 5 mathematical formulations of such local alignments. These formulations have been implemented and tested with CPLEX 10.0 package. Then, we developed an efficient dedicated algorithm to solve local alignments. Our algorithm uses well-known techniques from Operational Research: Branch & Bound, Subgradient Descent and Lagrangian Relaxation. We show that, despite greater complexity, local alignments using pairwise parameters are feasible and improve the quality of the alignments.
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https://tel.archives-ouvertes.fr/tel-00512725
Contributor : Guillaume Collet <>
Submitted on : Tuesday, August 31, 2010 - 2:01:09 PM
Last modification on : Friday, November 16, 2018 - 1:23:43 AM
Long-term archiving on : Thursday, December 1, 2016 - 2:56:37 PM

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  • HAL Id : tel-00512725, version 1

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Guillaume Collet. Alignements locaux pour la reconnaissance de repliements des protéines par programmation linéaire en nombres entiers. Modélisation et simulation. Université Rennes 1, 2010. Français. ⟨tel-00512725⟩

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