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An Alignment-Free Distance Measure for Closely Related Genomes

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Comparative Genomics (RECOMB-CG 2008)

Part of the book series: Lecture Notes in Computer Science ((LNBI,volume 5267))

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Abstract

Phylogeny reconstruction on a genome scale remains computationally challenging even for closely related organisms. Here we propose an alignment-free pairwise distance measure, K r, for genomes separated by less than approximately 0.5 mismatches/nucleotide. We have implemented the computation of K r based on enhanced suffix arrays in the program kr, which is freely available from guanine.evolbio.mpg.de/kr/. The software is applied to genomes obtained from three sets of taxa: 27 primate mitochondria, eight Staphylococcus agalactiae strains, and 12 Drosophila species. Subsequent clustering of the K r values always recovers phylogenies that are similar or identical to the accepted branching order.

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Author information

Authors and Affiliations

  1. Department of Evolutionary Genetics, Max-Planck-Institute for Evolutionary Biology, Plön, Germany

    Bernhard Haubold & Mirjana Domazet-Los̆o

  2. Faculty of Electrical Engineering and Computing, University of Zagreb, Zagreb, Croatia

    Mirjana Domazet-Los̆o

  3. Institute of Genetics, Universität zu Köln, Cologne, Germany

    Thomas Wiehe

Authors
  1. Bernhard Haubold
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  2. Mirjana Domazet-Los̆o
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  3. Thomas Wiehe
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Editor information

Editors and Affiliations

  1. Molecular and Cell Biology, University of Connecticut, Division of Genetics and Genomics, Beach Hall, 354 Mansfiled Rd, CT 06269, Storrs, USA

    Craig E. Nelson

  2. Université Paris-Est, IGM-LabInfo, 5 Bd Descartes, Champs sur Marne, 77454, Marne la Vallée, France

    Stéphane Vialette

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Haubold, B., Domazet-Los̆o, M., Wiehe, T. (2008). An Alignment-Free Distance Measure for Closely Related Genomes. In: Nelson, C.E., Vialette, S. (eds) Comparative Genomics. RECOMB-CG 2008. Lecture Notes in Computer Science(), vol 5267. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-87989-3_7

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  • DOI: https://doi.org/10.1007/978-3-540-87989-3_7

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-87988-6

  • Online ISBN: 978-3-540-87989-3

  • eBook Packages: Computer ScienceComputer Science (R0)

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