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A Tractable Variant of the Single Cut or Join Distance with Duplicated Genes

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Comparative Genomics (RECOMB-CG 2017)

Part of the book series: Lecture Notes in Computer Science ((LNBI,volume 10562))

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Abstract

In this work, we introduce a variant of the Single Cut or Join distance that accounts for duplicated genes, in the context of directed evolution from an ancestral genome to a descendant genome where orthology relations between ancestral genes and their descendant are known. Our model includes two duplication mechanisms: single-gene tandem duplication and creation of single-gene circular chromosomes. We prove that in this model, computing the distance and a parsimonious evolutionary scenario in terms of SCJ and single-gene duplication events can be done in linear time. Simulations show that the inferred number of cuts and joins scales linearly with the true number of such events even at high rates of genome rearrangements and segmental duplications. We also show that the median problem is tractable for this distance.

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Notes

  1. 1.

    We use the generic term “gene” here to identify a genomic locus.

  2. 2.

    https://github.com/acme92/SCJTDFD.

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Acknowledgments

CC is supported by a Discovery Grant from the Natural Sciences and Engineering Research Council of Canada. PF is supported by the Genome Canada grant PathoGiST.

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Authors and Affiliations

  1. School of Computing Science, Simon Fraser University, 8888 University Drive, Burnaby, BC, V5A 1S6, Canada

    Pedro Feijão

  2. Department of Mathematics, Simon Fraser University, 8888 University Drive, Burnaby, BC, V5A 1S6, Canada

    Aniket Mane & Cedric Chauve

Authors
  1. Pedro Feijão
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  2. Aniket Mane
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  3. Cedric Chauve
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Corresponding author

Correspondence to Cedric Chauve .

Editor information

Editors and Affiliations

  1. University of Campinas, Campinas, São Paulo, Brazil

    Joao Meidanis

  2. Rice University, Houston, Texas, USA

    Luay Nakhleh

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Feijão, P., Mane, A., Chauve, C. (2017). A Tractable Variant of the Single Cut or Join Distance with Duplicated Genes. In: Meidanis, J., Nakhleh, L. (eds) Comparative Genomics. RECOMB-CG 2017. Lecture Notes in Computer Science(), vol 10562. Springer, Cham. https://doi.org/10.1007/978-3-319-67979-2_2

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  • DOI: https://doi.org/10.1007/978-3-319-67979-2_2

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  • Publisher Name: Springer, Cham

  • Print ISBN: 978-3-319-67978-5

  • Online ISBN: 978-3-319-67979-2

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