The Reversal Median Problem, Common Intervals, and Mitochondrial Gene Orders

  • Matthias Bernt
  • Daniel Merkle
  • Martin Middendorf
Conference paper

DOI: 10.1007/11875741_6

Part of the Lecture Notes in Computer Science book series (LNCS, volume 4216)
Cite this paper as:
Bernt M., Merkle D., Middendorf M. (2006) The Reversal Median Problem, Common Intervals, and Mitochondrial Gene Orders. In: R. Berthold M., Glen R.C., Fischer I. (eds) Computational Life Sciences II. CompLife 2006. Lecture Notes in Computer Science, vol 4216. Springer, Berlin, Heidelberg

Abstract

An important problem for phylogenetic investigations that are based on gene orders is to find for three given gene orders a fourth gene order that has a minimum sum of reversal distances to the three given gene orders. This problem is called Reversal Median problem (RMP). The RMP is studied here under the constraint that common (combinatorial) structures are preserved which are modeled as common intervals. An existing branch-and-bound algorithm for RMP is extended here so that it can solve the RMP with common intervals optimally. This algorithm is applied to mitochondrial gene order data for different animal taxa. It is shown that common intervals occur often for most taxa and that many common intervals are destroyed when the RMP is solved optimally with standard methods that do not consider common intervals.

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Copyright information

© Springer-Verlag Berlin Heidelberg 2006

Authors and Affiliations

  • Matthias Bernt
    • 1
  • Daniel Merkle
    • 1
  • Martin Middendorf
    • 1
  1. 1.Parallel Computing and Complex Systems Group, Department of Computer ScienceUniversity of LeipzigGermany

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