Algorithms to Detect Multiprotein Modularity Conserved during Evolution

  • Luqman Hodgkinson
  • Richard M. Karp
Part of the Lecture Notes in Computer Science book series (LNCS, volume 6674)

Abstract

Detecting essential multiprotein modules that change infrequently during evolution is a challenging algorithmic task that is important for understanding the structure, function, and evolution of the biological cell. In this paper, we present a linear-time algorithm, Produles, that improves on the running time of previous algorithms. We present a biologically motivated graph theoretic set of algorithm goals complementary to previous evaluation measures, demonstrate that Produles attains these goals more comprehensively than previous algorithms, and exhibit certain recurrent anomalies in the performance of previous algorithms that are not detected by previous measures.

Keywords

modularity interactomes evolution algorithms 

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Copyright information

© Springer-Verlag Berlin Heidelberg 2011

Authors and Affiliations

  • Luqman Hodgkinson
    • 1
    • 2
    • 3
  • Richard M. Karp
    • 1
    • 2
    • 3
  1. 1.Computer Science DivisionUniversity of CaliforniaBerkeleyUSA
  2. 2.Center for Computational BiologyUniversity of CaliforniaBerkeleyUSA
  3. 3.International Computer Science InstituteUSA

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