HP Distance Via Double Cut and Join Distance

  • Anne Bergeron
  • Julia Mixtacki
  • Jens Stoye
Part of the Lecture Notes in Computer Science book series (LNCS, volume 5029)


The genomic distance problem in the Hannenhalli-Pevzner theory is the following: Given two genomes whose chromosomes are linear, calculate the minimum number of inversions and translocations that transform one genome into the other. This paper presents a new distance formula based on a simple tree structure that captures all the delicate features of this problem in a unifying way.


Adjacency Graph Unoriented Component White Leaf Grey Node Grey Leaf 
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.
    Bergeron, A.: A very elementary presentation of the hannenhalli-pevzner theory. In: Amir, A., Landau, G.M. (eds.) CPM 2001. LNCS, vol. 2089, pp. 106–117. Springer, Heidelberg (2001)Google Scholar
  2. 2.
    Bergeron, A., Mixtacki, J., Stoye, J.: Reversal distance without hurdles and fortresses. In: Sahinalp, S.C., Muthukrishnan, S.M., Dogrusoz, U. (eds.) CPM 2004. LNCS, vol. 3109, pp. 388–399. Springer, Heidelberg (2004)Google Scholar
  3. 3.
    Bergeron, A., Mixtacki, J., Stoye, J.: On sorting by translocations. J. Comput. Biol. 13(2), 567–578 (2006)CrossRefMathSciNetGoogle Scholar
  4. 4.
    Bergeron, A., Mixtacki, J., Stoye, J.: A unifying view of genome rearrangements. In: Bücher, P., Moret, B.M.E. (eds.) WABI 2006. LNCS (LNBI), vol. 4175, pp. 163–173. Springer, Heidelberg (2006)CrossRefGoogle Scholar
  5. 5.
    Bergeron, A., Stoye, J.: On the similarity of sets of permutations and its applications to genome comparison. In: Warnow, T., Zhu, B. (eds.) COCOON 2003. LNCS, vol. 2697, pp. 68–79. Springer, Heidelberg (2003)CrossRefGoogle Scholar
  6. 6.
    Hannenhalli, S., Pevzner, P.A.: Transforming men into mice (polynomial algorithm for genomic distance problem). In: Proceedings of FOCS 1995, pp. 581–592. IEEE Press, Los Alamitos (1995)Google Scholar
  7. 7.
    Jean, G., Nikolski, M.: Genome rearrangements: a correct algorithm for optimal capping. Inf. Process. Lett. 104, 14–20 (2007)CrossRefMathSciNetGoogle Scholar
  8. 8.
    Ozery-Flato, M., Shamir, R.: Two notes on genome rearrangements. J. Bioinf. Comput. Biol. 1(1), 71–94 (2003)CrossRefGoogle Scholar
  9. 9.
    Tesler, G.: Efficient algorithms for multichromosomal genome rearrangements. J. Comput. Syst. Sci. 65(3), 587–609 (2002)zbMATHCrossRefMathSciNetGoogle Scholar
  10. 10.
    Tesler, G.: GRIMM: Genome rearrangements web server. Bioinformatics 18(3), 492–493 (2002)CrossRefMathSciNetGoogle Scholar
  11. 11.
    Yancopoulos, S., Attie, O., Friedberg, R.: Efficient sorting of genomic permutations by translocation, inversion and block interchange. Bioinformatics 21(16), 3340–3346 (2005)CrossRefGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2008

Authors and Affiliations

  • Anne Bergeron
    • 1
  • Julia Mixtacki
    • 2
  • Jens Stoye
    • 3
  1. 1.Dépt. d’informatiqueUniversité du Québec à MontréalCanada
  2. 2.International NRW Graduate School in Bioinformatics and Genome ResearchUniversität BielefeldGermany
  3. 3.Technische FakultätUniversität BielefeldGermany

Personalised recommendations