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DOI: 10.4230/OASIcs.GCB.2013.24

Alignment-free sequence comparison with spaced k-mers

Authors: Marcus Boden, Martin Schöneich, Sebastian Horwege, Sebastian Lindner, Chris Leimeister, and Burkhard Morgenstern

Published in: OASIcs, Volume 34, German Conference on Bioinformatics 2013

Abstract

Alignment-free methods are increasingly used for genome analysis and phylogeny reconstruction since they circumvent various difficulties of traditional approaches that rely on multiple sequence alignments. In particular, they are much faster than alignment-based methods. Most alignment-free approaches work by analyzing the k-mer composition of sequences. In this paper, we propose to use 'spaced k-mers', i.e. patterns of deterministic and 'don't care' positions instead of contiguous k-mers. Using simulated and real-world sequence data, we demonstrate that this approach produces better phylogenetic trees than alignment-free methods that rely on contiguous k-mers. In addition, distances calculated with spaced k-mers appear to be statistically more stable than distances based on contiguous k-mers.

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Marcus Boden, Martin Schöneich, Sebastian Horwege, Sebastian Lindner, Chris Leimeister, and Burkhard Morgenstern. Alignment-free sequence comparison with spaced k-mers. In German Conference on Bioinformatics 2013. Open Access Series in Informatics (OASIcs), Volume 34, pp. 24-34, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2013)

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@InProceedings{boden_et_al:OASIcs.GCB.2013.24,
  author =	{Boden, Marcus and Sch\"{o}neich, Martin and Horwege, Sebastian and Lindner, Sebastian and Leimeister, Chris and Morgenstern, Burkhard},
  title =	{{Alignment-free sequence comparison with spaced k-mers}},
  booktitle =	{German Conference on Bioinformatics 2013},
  pages =	{24--34},
  series =	{Open Access Series in Informatics (OASIcs)},
  ISBN =	{978-3-939897-59-0},
  ISSN =	{2190-6807},
  year =	{2013},
  volume =	{34},
  editor =	{Bei{\ss}barth, Tim and Kollmar, Martin and Leha, Andreas and Morgenstern, Burkhard and Schultz, Anne-Kathrin and Waack, Stephan and Wingender, Edgar},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/OASIcs.GCB.2013.24},
  URN =		{urn:nbn:de:0030-drops-42334},
  doi =		{10.4230/OASIcs.GCB.2013.24},
  annote =	{Keywords: Alignment-free sequence comparison, phylogeny reconstruction}
}

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Alignment-free sequence comparison with spaced k-mers

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