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On Computing the Breakpoint Reuse Rate in Rearrangement Scenarios

  • Anne Bergeron
  • Julia Mixtacki
  • Jens Stoye
Part of the Lecture Notes in Computer Science book series (LNCS, volume 5267)

Abstract

In the past years, many combinatorial arguments have been made to support the theory that mammalian genome rearrangement scenarios rely heavily on breakpoint reuse. Different models of genome rearrangements have been suggested, from the classical set of operations that include inversions, translocations, fusions and fissions, to more elaborate models that include transpositions. Here we show that the current definition of breakpoint reuse rate is based on assumptions that are seldom true for mammalian genomes, and propose a new approach to compute this parameter. We explore the formal properties of this new measure and apply these results to the human-mouse genome comparison. We show that the reuse rate is intimately linked to a particular rearrangement scenario, and that the reuse rate can vary from 0.89 to 1.51 for scenarios of the same length that transform the mouse genome into the human genome, where a rate of 1 indicates no reuse at all.

Keywords

Mouse Genome Genome Rearrangement Adjacency Graph Circular Chromosome Linear Chromosome 
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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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

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