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Using Dominances for Solving the Protein Family Identification Problem

  • Noel Malod-Dognin
  • Mathilde Le Boudic-Jamin
  • Pritish Kamath
  • Rumen Andonov
Part of the Lecture Notes in Computer Science book series (LNCS, volume 6833)

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.

Keywords

Protein structure comparison classification bounds dominance 

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Copyright information

© Springer-Verlag Berlin Heidelberg 2011

Authors and Affiliations

  • Noel Malod-Dognin
    • 1
  • Mathilde Le Boudic-Jamin
    • 2
  • Pritish Kamath
    • 3
  • Rumen Andonov
    • 2
  1. 1.INRIA Sophia Antipolis - MéditerranéeFrance
  2. 2.INRIA Rennes - Bretagne Atlantique and University of Rennes 1France
  3. 3.Computer Science and Engineering DepartmentIndian Institute of TechnologyIndia

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