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A Framework for Orthology Assignment from Gene Rearrangement Data

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Comparative Genomics (RCG 2005)

Part of the book series: Lecture Notes in Computer Science ((LNBI,volume 3678))

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Abstract

Gene rearrangements have been used successfully in phylogenetic reconstruction and comparative genomics, but usually under the assumption that all genomes have the same gene content and that no gene is duplicated. While these assumptions allow one to work with organellar genomes, they are too restrictive for nuclear genomes. The main challenge in handling more realistic data is how to deal with gene families, specifically, how to identify orthologs. While searching for orthologies is a common task in computational biology, it is usually done using sequence data. Sankoff first addressed the problem in 1999, introducing the notion of exemplar, but his approach uses an NP-hard optimization step to discard all but one member (the exemplar) of each gene family, losing much valuable information in the process. We approach the problem using all available data in the gene orders and gene families, provide an optimization framework in which to phrase the problem, and present some preliminary theoretical results.

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Authors and Affiliations

  1. Department of Computer Science, University of New Mexico, Albuquerque, NM, 87131, USA

    Krister M. Swenson, Nicholas D. Pattengale & B. M. E. Moret

Authors
  1. Krister M. Swenson
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  2. Nicholas D. Pattengale
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  3. B. M. E. Moret
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Editor information

Editors and Affiliations

  1. University of Dublin, Smurfit Institute of Genetics, Trinity College, Ireland

    Aoife McLysaght

  2. Center for Bioinformatics ZBIT, Tübingen University, Sand 14, 72076, Tübingen, Germany

    Daniel H. Huson

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© 2005 Springer-Verlag Berlin Heidelberg

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Swenson, K.M., Pattengale, N.D., Moret, B.M.E. (2005). A Framework for Orthology Assignment from Gene Rearrangement Data. In: McLysaght, A., Huson, D.H. (eds) Comparative Genomics. RCG 2005. Lecture Notes in Computer Science(), vol 3678. Springer, Berlin, Heidelberg. https://doi.org/10.1007/11554714_14

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  • DOI: https://doi.org/10.1007/11554714_14

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-28932-6

  • Online ISBN: 978-3-540-31814-9

  • eBook Packages: Computer ScienceComputer Science (R0)

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