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Using Dominances for Solving the Protein Family Identification Problem

Noël Malod-Dognin 1 Mathilde Le Boudic-Jamin 2 Pritish Kamath 3 Rumen Andonov 2, * 
* Corresponding author
1 ABS - Algorithms, Biology, Structure
CRISAM - Inria Sophia Antipolis - Méditerranée
2 SYMBIOSE - Biological systems and models, bioinformatics and sequences
IRISA - Institut de Recherche en Informatique et Systèmes Aléatoires, Inria Rennes – Bretagne Atlantique
Abstract : 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.
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Submitted on : Tuesday, July 19, 2011 - 9:36:39 AM
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Noël Malod-Dognin, Mathilde Le Boudic-Jamin, Pritish Kamath, Rumen Andonov. Using Dominances for Solving the Protein Family Identification Problem. 11th Workshop on Algorithms in Bioinformatics (WABI 2011), Max-Planck-Institute für Informatics, Sep 2011, Saarbrücken, Germany. pp.201-212, ⟨10.1007/978-3-642-23038-7_18⟩. ⟨inria-00609432⟩



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