The Problem of Chromosome Reincorporation in DCJ Sorting and Halving

  • Jakub Kováč
  • Marília D. V. Braga
  • Jens Stoye
Part of the Lecture Notes in Computer Science book series (LNCS, volume 6398)


We study two problems in the double cut and join (DCJ) model: sorting – transforming one multilinear genome into another and halving – transforming a duplicated genome into a perfectly duplicated one. The DCJ model includes rearrangement operations such as reversals, translocations, fusions and fissions. We can also mimic transpositions or block interchanges by two operations: we extract an appropriate segment of a chromosome, creating a temporary circular chromosome, and in the next step we reinsert it in its proper place. Existing linear-time algorithms solving both problems ignore the constraint of reincorporating the temporary circular chromosomes immediately after their creation. For the restricted sorting problem only a quadratic algorithm was known, whereas the restricted halving problem was stated as open by Tannier, Zheng, and Sankoff. In this paper we address this constraint and show how to solve the problem of sorting in O(nlogn) time and halving in O(n 3/2) time.


Adjacency Graph Circular Chromosome Linear Chromosome Linear Genome Duplicate Genome 
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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© Springer-Verlag Berlin Heidelberg 2010

Authors and Affiliations

  • Jakub Kováč
    • 1
    • 2
  • Marília D. V. Braga
    • 2
  • Jens Stoye
    • 2
  1. 1.Department of Computer ScienceComenius UniversitySlovakia
  2. 2.AG Genominformatik, Technische FakultätUniversität BielefeldGermany

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