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Perfect DCJ Rearrangement

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Comparative Genomics (RECOMB-CG 2008)

Part of the book series: Lecture Notes in Computer Science ((LNBI,volume 5267))

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Abstract

We study the problem of transforming a multichromosomal genome into another using Double-Cut-and-Join (DCJ) operations. We introduce the notion of DCJ scenario that does not break families of common intervals (groups of genes co-localized in both genomes). Such scenarios are called perfect, and generalize the notion of perfect reversal scenarios. While perfect sorting by reversals is NP-hard if the family of common intervals is nested, we show that finding a shortest perfect DCJ scenario can be answered in polynomial time in this case. Moreover, while perfect sorting by reversals is easy when the family of common intervals is weakly separable, we show that the corresponding problem is NP-hard in the DCJ case. These contrast with previous comparisons between the reversal and DCJ models, that showed that most problems have similar complexity in both models.

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Author information

Authors and Affiliations

  1. Université Montpellier 2, UMR AMAP, Montpellier, F-34000, France

    Sèverine Bérard

  2. CNRS, LIRMM, CNRS UMR55076, Université Montpellier 2, Montpellier, France

    Sèverine Bérard, Annie Chateau & Christophe Paul

  3. Department of Mathematics, Simon Fraser University, Burnaby, (BC), Canada

    Cedric Chauve

  4. INRIA, LBBE, CNRS UMR5558, Université de Lyon 1, Villeurbanne, France

    Eric Tannier

Authors
  1. Sèverine Bérard
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  2. Annie Chateau
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  3. Cedric Chauve
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  4. Christophe Paul
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  5. Eric Tannier
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Editor information

Editors and Affiliations

  1. Molecular and Cell Biology, University of Connecticut, Division of Genetics and Genomics, Beach Hall, 354 Mansfiled Rd, CT 06269, Storrs, USA

    Craig E. Nelson

  2. Université Paris-Est, IGM-LabInfo, 5 Bd Descartes, Champs sur Marne, 77454, Marne la Vallée, France

    Stéphane Vialette

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© 2008 Springer-Verlag Berlin Heidelberg

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Bérard, S., Chateau, A., Chauve, C., Paul, C., Tannier, E. (2008). Perfect DCJ Rearrangement. In: Nelson, C.E., Vialette, S. (eds) Comparative Genomics. RECOMB-CG 2008. Lecture Notes in Computer Science(), vol 5267. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-87989-3_12

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  • DOI: https://doi.org/10.1007/978-3-540-87989-3_12

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-87988-6

  • Online ISBN: 978-3-540-87989-3

  • eBook Packages: Computer ScienceComputer Science (R0)

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