Sorting Genomes with Insertions, Deletions and Duplications by DCJ

  • Sophia Yancopoulos
  • Richard Friedberg
Part of the Lecture Notes in Computer Science book series (LNCS, volume 5267)


We extend the DCJ paradigm to perform genome rearrangments on pairs of genomes having unequal gene content and/or multiple copies by permitting genes in one genome which are completely or partially unmatched in the other. The existence of unmatched gene ends introduces new kinds of paths in the adjacency graph, since some paths can now terminate internal to a chromosome and not on telomeres. We introduce Òghost adjacenciesÓ to supply the missing gene ends in the genome not containing them. Ghosts enable us to close paths that were due to incomplete matching, just as null points enable us to close even paths terminating in telomeres. We define generalalized DCJ operations on the generalized adjacency graph, and give a prescription for calculating the DCJ distance for the expanded repertoire of operations which includes insertions, deletions and duplications.


Triangle Inequality Null Point Target Genome Adjacency Graph Circular Chromosome 
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  1. 1.
    Kent, W.J., Baertsch, R., Hinrichs, A., Miller, W., Haussler, D.: Evolutions cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proc. Natl Acad. Sci. USA 100, 11484–11489 (2003)CrossRefGoogle Scholar
  2. 2.
    El-Mabrouk, N.: Sorting signed permutations by reversals and insertions/deletions of contiguous segments. Journal of Discrete Algorithms 1(1), 105–122 (2001)MathSciNetGoogle Scholar
  3. 3.
    Marron, M., Swenson, K., Moret, B.: Genomic distances under deletions and insertions. Theoretical Computer Science 325(3), 347–360 (2004)zbMATHCrossRefMathSciNetGoogle Scholar
  4. 4.
    Yancopoulos, S., Attie, O., Friedberg, R.: Efficient sorting of genomic permutations by translocation, inversion and block interchange. Bioinformatics 21, 3340–3346 (2005)CrossRefGoogle Scholar
  5. 5.
    Feuk, L., Carson, A.R., Scherer, S.W.: Structural variation in the human genome. Nat. Rev. Genet. Feb. 7(2), 85–97 (2006)CrossRefGoogle Scholar
  6. 6.
    The Chimpanzee Sequencing and Analysis Consortium, Initial sequence of the chimpanzee genome and comparison with the human genome. Nature 437, 69–87 (2005)Google Scholar
  7. 7.
    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
  8. 8.
    Bergeron communicationGoogle Scholar
  9. 9.
    Bafna, V., Pevzner, P.A.: Genome rearrangements and sorting by reversals. In: Proc. 34th Ann. IEEE Symp Found. Comp. Sci., pp. 148–157. IEEE Press, Los Alamitos (1993)Google Scholar
  10. 10.
    Friedberg, R., Darling, A.E., Yancopoulos, S.: Genome Rearrangement by the Double Cut and Join Operation. In: Keith, J.M. (ed.) Bioinformatics, Data, Sequence Analysis and Evolution, ch. 18. vol. I. Humana Press (2008)Google Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2008

Authors and Affiliations

  • Sophia Yancopoulos
    • 1
  • Richard Friedberg
    • 2
  1. 1.The Feinstein Institute for Medical ResearchManhassetUSA
  2. 2.Department of PhysicsColumbia UniversityNYUSA

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