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On the Similarity of Sets of Permutations and Its Applications to Genome Comparison

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Computing and Combinatorics (COCOON 2003)

Part of the book series: Lecture Notes in Computer Science ((LNCS,volume 2697))

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Abstract

The comparison of genomes with the same gene content relies on our ability to compare permutations, either by measuring how much they differ, or by measuring how much they are alike. With the notable exception of the breakpoint distance, which is based on the concept of conserved adjacencies, measures of distance do not generalize easily to sets of more than two permutations. In this paper, we present a basic unifying notion, conserved intervals, as a powerful generalization of adjacencies, and as a key feature of genome rearrangement theories. We also show that sets of conserved intervals have elegant nesting and chaining properties that allow the development of compact graphic representations, and linear time algorithms to manipulate them.

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Author information

Authors and Affiliations

  1. LaCIM, Université du Québec à Montréal, Canada

    Anne Bergeron

  2. Technische Fakultät, Universität Bielefeld, Germany

    Jens Stoye

Authors
  1. Anne Bergeron
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  2. Jens Stoye
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Editor information

Editors and Affiliations

  1. Department of Computer Science, University of Texas at Austin, One University Station, C0500, Austin, TX, 78712, USA

    Tandy Warnow

  2. Department of Computer Science, Montana State University, EPS 357, Bozeman, MT, 59717, USA

    Binhai Zhu

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Bergeron, A., Stoye, J. (2003). On the Similarity of Sets of Permutations and Its Applications to Genome Comparison. In: Warnow, T., Zhu, B. (eds) Computing and Combinatorics. COCOON 2003. Lecture Notes in Computer Science, vol 2697. Springer, Berlin, Heidelberg. https://doi.org/10.1007/3-540-45071-8_9

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  • DOI: https://doi.org/10.1007/3-540-45071-8_9

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  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-40534-4

  • Online ISBN: 978-3-540-45071-9

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