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Models and Algorithms for Genome Rearrangement with Positional Constraints

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Algorithms in Bioinformatics (WABI 2015)

Part of the book series: Lecture Notes in Computer Science ((LNBI,volume 9289))

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Abstract

Traditionally, the merit of a rearrangement scenario between two genomes has been measured based on a parsimony criteria alone; two scenarios with the same number of rearrangements are considered equally good. In this paper, we acknowledge that each rearrangement has a certain likelihood of occurring based on biological constraints, e.g. physical proximity of the DNA segments implicated, or repetitive sequences. Accordingly, we propose optimization problems with the objective of maximizing overall likelihood, by weighting the rearrangements. We study a binary weight function suitable to the representation of sets of genome positions that are most likely to have swapped adjacencies. We give a polynomial-time algorithm for the problem of finding a minimum weight double cut and join (DCJ) scenario among all minimum length scenarios. In the process, we solve an optimization problem on colored noncrossing partitions which is a generalization of the Maximum Independent Set problem on circle graphs.

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Acknowledgments

We would like to thank Anne Bergeron for her helpful comments during the preparation of this manuscript. This work was funded in part by a grant from the Fonds de Recherche du Québec en Nature et Technologies.

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Authors and Affiliations

  1. CNRS, LIRMM, Université de Montpellier, Montpellier, France

    Krister M. Swenson

  2. Institut de Biologie Computationnelle (IBC), Montpellier, France

    Krister M. Swenson

  3. McGill University, Montreal, QC, Canada

    Mathieu Blanchette

Authors
  1. Krister M. Swenson
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  2. Mathieu Blanchette
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Correspondence to Krister M. Swenson .

Editor information

Editors and Affiliations

  1. University of Maryland, College Park, Maryland, USA

    Mihai Pop

  2. University of Lille, Lille, France

    Hélène Touzet

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Swenson, K.M., Blanchette, M. (2015). Models and Algorithms for Genome Rearrangement with Positional Constraints. In: Pop, M., Touzet, H. (eds) Algorithms in Bioinformatics. WABI 2015. Lecture Notes in Computer Science(), vol 9289. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-662-48221-6_18

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  • DOI: https://doi.org/10.1007/978-3-662-48221-6_18

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  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-662-48220-9

  • Online ISBN: 978-3-662-48221-6

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