Decompositions of Multiple Breakpoint Graphs and Rapid Exact Solutions to the Median Problem

  • Andrew Wei Xu
  • David Sankoff
Part of the Lecture Notes in Computer Science book series (LNCS, volume 5251)

Abstract

The median genome problem reduces to a search for the vertex matching in the multiple breakpoint graph (MBG) that maximizes the number of alternating colour cycles formed with the matchings representing the given genomes. We describe a class of “adequate” subgraphs of MBGs that allow a decomposition of an MBG into smaller, more easily solved graphs. We enumerate all of these graphs up to a certain size and incorporate the search for them into an exhaustive algorithm for the median problem. This enables a dramatic speedup in most randomly generated instances with hundreds or even thousands of vertices, as long as the ratio of genome rearrangements to genome size is not too large.

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Copyright information

© Springer-Verlag Berlin Heidelberg 2008

Authors and Affiliations

  • Andrew Wei Xu
    • 1
  • David Sankoff
    • 1
  1. 1.Department of Mathematics and StatisticsUniversity of OttawaCanada

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