Using Dominances for Solving the Protein Family Identification Problem
نویسندگان
چکیده
Identification of protein families is a computational biology challenge that needs efficient and reliable methods. Here we introduce the concept of dominance and propose a novel combined approach based on Distance Alignment Search Tool (DAST), which contains an exact algorithm with bounds. Our experiments show that this method successfully finds the most similar proteins in a set without solving all instances. Key-words: Protein structure comparison, classification, bounds, dominance ∗ A.B.S., INRIA Sophia Antipolis Méditerranée, France. † Symbiose, INRIA Rennes Bretagne Atlantique, France. ‡ Computer Science and Engineering Department, Indian Institute of Technology, India. in ria -0 06 09 43 2, v er si on 1 19 J ul 2 01 1 Utilisation de la dominance pour l’identification de familles protéiques Résumé : L’identification des familles protéique est un challenge de la biologie computationnelle qui nécessite des méthodes efficaces et robustes. Nous introduisons ici le concept de dominance entre instance de comparaison de structures prot’eiques, et proposons une nouvelle approche basée sur DAST (Distance Alignment Search Tool), un algorithme exact auquel nous rajoutons des bornes. Les résultats obtenus montrent que notre méthode résout correctement le problème de l’identification des familles protéique sans avoir besoin de résoudre toutes les instances de comparaison de structures. Mots-clés : Comparaison de structure protéique, classification, bornes, dominance in ria -0 06 09 43 2, v er si on 1 19 J ul 2 01 1 Using Dominances for Solving the Protein Family Identification Problem 3
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