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Sorting by Cuts, Joins and Whole Chromosome Duplications

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Combinatorial Pattern Matching (CPM 2015)

Part of the book series: Lecture Notes in Computer Science ((LNTCS,volume 9133))

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Abstract

Genome rearrangement problems have been extensively studied due to their importance in biology. Most studied models assumed a single copy per gene. However, in reality duplicated genes are common, most notably in cancer. Here we make a step towards handling duplicated genes by considering a model that allows the atomic operations of cut, join and whole chromosome duplication. Given two linear genomes, \(\varGamma \) with one copy per gene, and \(\varDelta \) with two copies per gene, we give a linear time algorithm for computing a shortest sequence of operations transforming \(\varGamma \) into \(\varDelta \) such that all intermediate genomes are linear. We also show that computing an optimal sequence with fewest duplications is NP-hard.

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Acknowledgments

We thank our referees for many helpful and insightful comments. This study was supported by the Israeli Science Foundation (grant 317/13) and the Dotan Hemato-Oncology Research Center at Tel Aviv University. RZ was supported in part by fellowships from the Edmond J. Safra Center for Bioinformatics at Tel Aviv University and from the Israeli Center of Research Excellence (I-CORE) Gene Regulation in Complex Human Disease (Center No 41/11).

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Authors and Affiliations

  1. Tel-Aviv University, 69978, Tel-Aviv, Israel

    Ron Zeira & Ron Shamir

Authors
  1. Ron Zeira
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  2. Ron Shamir
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Correspondence to Ron Zeira .

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Editors and Affiliations

  1. Department of Computer Science, University of Verona, Verona, Italy

    Ferdinando Cicalese

  2. Department of Computer Science, Bar-Ilan University, Ramat Gan, Israel

    Ely Porat

  3. Department of Computer Science, University of Salerno, Fisciano, Italy

    Ugo Vaccaro

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Zeira, R., Shamir, R. (2015). Sorting by Cuts, Joins and Whole Chromosome Duplications. In: Cicalese, F., Porat, E., Vaccaro, U. (eds) Combinatorial Pattern Matching. CPM 2015. Lecture Notes in Computer Science(), vol 9133. Springer, Cham. https://doi.org/10.1007/978-3-319-19929-0_34

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  • DOI: https://doi.org/10.1007/978-3-319-19929-0_34

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  • Publisher Name: Springer, Cham

  • Print ISBN: 978-3-319-19928-3

  • Online ISBN: 978-3-319-19929-0

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