A Parallel Algorithm for Solving the Reversal Median Problem

  • Matthias Bernt
  • Daniel Merkle
  • Martin Middendorf
Part of the Lecture Notes in Computer Science book series (LNCS, volume 3911)


We present a new algorithm called rEvoluzer II for solving the Reversal Median problem (RMP). Similar to its predecessor rEvoluzer I the new algorithm can preserve conserved intervals but it has the additional property that it is suitable for parallelization. For the parallel version of rEvoluzer II a master-slave parallelization scheme is used and several methods for reducing parallelization overheads have been incorporated. We show experimentally that rEvoluzer achieves very good results compared to other methods for the RMP. It is also shown that the parallel version has good scaling behavior for a not too large number of processors.


Parallel Algorithm Parallel Version Master Node Chunk Size Master Process 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.


Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.


  1. 1.
    Bérard, S., Bergeron, A., Chauve, C.: Conservation of combinatorial structures in evolution scenarios. In: Lagergren, J. (ed.) RECOMB-WS 2004. LNCS (LNBI), vol. 3388, pp. 1–14. Springer, Heidelberg (2005)CrossRefGoogle Scholar
  2. 2.
    Bergeron, A., Blanchette, M., Chateau, A., Chauve, C.: Reconstructing ancestral gene orders using conserved intervals. In: Jonassen, I., Kim, J. (eds.) WABI 2004. LNCS (LNBI), vol. 3240, pp. 14–45. Springer, Heidelberg (2004)CrossRefGoogle Scholar
  3. 3.
    Bergeron, A., Luc, N., Raffinot, M., Risler, J.: Gene teams: a new formalization of gene clusters for comparative genomics. Computational Biology and Chemistry 27(1), 59–67 (2003)CrossRefGoogle Scholar
  4. 4.
    Bergeron, A., Stoye, J.: On the similarity of sets of permutations and its applications to genome comparison. In: Warnow, T.J., Zhu, B. (eds.) COCOON 2003. LNCS, vol. 2697, pp. 68–79. Springer, Heidelberg (2003)CrossRefGoogle Scholar
  5. 5.
    Bernt, M., Merkle, D., Middendorf, M.: Genome rearrangement based on reversals that preserve conserved intervals. IEEE Transactions on Bioinformatics (accepted, 2005)Google Scholar
  6. 6.
    Bourque, G., Pevzner, P.: Genome-Scale Evolution: Reconstructing Gene Orders in the Ancestral Species. Genome Res. 12(1), 26–36 (2002)Google Scholar
  7. 7.
    Caprara, A.: The reversal median problem. INFORMS Journal on Computing 15(1), 93–113 (2003)MathSciNetCrossRefzbMATHGoogle Scholar
  8. 8.
    Heber, S., Stoye, J.: Finding all common intervals of k permutations. In: Amir, A., Landau, G.M. (eds.) CPM 2001. LNCS, vol. 2089, pp. 207–218. Springer, Heidelberg (2001)CrossRefGoogle Scholar
  9. 9.
    Moret, B., Siepel, A.: Finding an optimal inversion median: Experimental results. In: Gascuel, O., Moret, B.M.E. (eds.) WABI 2001. LNCS, vol. 2149, pp. 189–203. Springer, Heidelberg (2001)CrossRefGoogle Scholar
  10. 10.
    Moret, B., Wyman, S., Bader, D.A., Warnow, T., Yan, M.: A new implementation and detailed study of breakpoint analysis. In: Proc. 6th Pacific Symp. on Biocomputing (PSB 2001), World Scientific Pub., Singapore (2001)Google Scholar
  11. 11.
    Sankoff, D.: Short inversions and conserved gene cluster. Bioinformatics 18(10), 1305–1308 (2002)CrossRefGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2006

Authors and Affiliations

  • Matthias Bernt
    • 1
  • Daniel Merkle
    • 1
  • Martin Middendorf
    • 1
  1. 1.Department of Computer ScienceUniversity of LeipzigGermany

Personalised recommendations