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A Probabilistic Model for Gene Content Evolution with Duplication, Loss, and Horizontal Transfer

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Research in Computational Molecular Biology (RECOMB 2006)

Part of the book series: Lecture Notes in Computer Science ((LNBI,volume 3909))

Abstract

We introduce a Markov model for the evolution of a gene family along a phylogeny. The model includes parameters for the rates of horizontal gene transfer, gene duplication, and gene loss, in addition to branch lengths in the phylogeny. The likelihood for the changes in the size of a gene family across different organisms can be calculated in O(N+hM 2) time and O(N+M 2) space, where N is the number of organisms, h is the height of the phylogeny, and M is the sum of family sizes. We apply the model to the evolution of gene content in Proteobacteria using the gene families in the COG (Clusters of Orthologous Groups) database.

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Author information

Authors and Affiliations

  1. Department of Computer Science and Operations Research, Université de Montréal, C.P. 6128, succ. Centre-Ville, Montréal, Québec, H3C 3J7, Canada

    Miklós Csűrös

  2. Department of Plant Taxonomy and Ecology, Eötvös Lóránd University, 1117 Budapest, Pázmány Péter Sétány 1/c, Hungary

    István Miklós

Authors
  1. Miklós Csűrös
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  2. István Miklós
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Editor information

Editors and Affiliations

  1. Georgia Institute of Technology and Università di Padova,  

    Alberto Apostolico

  2. Topic Chairs, P.O. Box

    Concettina Guerra

  3. Center for Molecular Biology and Computer Sciecne Department, Brown University, 115 Waterman St., 02912, Providence, RI, USA

    Sorin Istrail

  4. University of California, San Diego, USA

    Pavel A. Pevzner

  5. Department of Molecular and Computational Biology, University of Southern California, 1050 Childs Way, 90089-2910, Los Angeles, CA, USA

    Michael Waterman

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© 2006 Springer-Verlag Berlin Heidelberg

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Csűrös, M., Miklós, I. (2006). A Probabilistic Model for Gene Content Evolution with Duplication, Loss, and Horizontal Transfer. In: Apostolico, A., Guerra, C., Istrail, S., Pevzner, P.A., Waterman, M. (eds) Research in Computational Molecular Biology. RECOMB 2006. Lecture Notes in Computer Science(), vol 3909. Springer, Berlin, Heidelberg. https://doi.org/10.1007/11732990_18

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  • DOI: https://doi.org/10.1007/11732990_18

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-33295-4

  • Online ISBN: 978-3-540-33296-1

  • eBook Packages: Computer ScienceComputer Science (R0)

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