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Genomic Distance with DCJ and Indels

  • Marília D. V. Braga
  • Eyla Willing
  • Jens Stoye
Part of the Lecture Notes in Computer Science book series (LNCS, volume 6293)

Abstract

The double cut and join (DCJ) operation, introduced by Yancopoulos, Attie and Friedberg in 2005, allows one to represent most rearrangement events in genomes. However, a DCJ cannot perform an insertion or a deletion and most approaches under this model consider only genomes with the same content and without duplications, including the linear time algorithms to compute the DCJ distance and to find an optimal DCJ sorting sequence. In this work, we compare two genomes with unequal content, but still without duplications, and present a new linear time algorithm to compute the genomic distance, considering DCJ and indel operations. With this method we find preliminary evidence of the occurrence of clusters of deletions in the Rickettsia bacterium.

Keywords

Linear Time Algorithm Adjacency Graph Spotted Fever Circular Chromosome Genomic Distance 
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.

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References

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    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
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    Braga, M.D.V., Stoye, J.: The solution space of sorting by DCJ. To appear in Journal of Computational Biology (2010)Google Scholar
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    Yancopoulos, S., Friedberg, R.: Sorting Genomes with Insertions, Deletions and Duplications by DCJ. In: Nelson, C.E., Vialette, S. (eds.) RECOMB-CG 2008. LNCS (LNBI), vol. 5267, pp. 170–183. Springer, Heidelberg (2008)CrossRefGoogle Scholar
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Copyright information

© Springer-Verlag Berlin Heidelberg 2010

Authors and Affiliations

  • Marília D. V. Braga
    • 1
  • Eyla Willing
    • 1
  • Jens Stoye
    • 1
  1. 1.Technische FakultätUniversität BielefeldGermany

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