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DOI: 10.4230/OASIcs.GCB.2013.110

Avoiding Ambiguity and Assessing Uniqueness in Minisatellite Alignment

Authors: Benedikt Löwes and Robert Giegerich

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

Abstract

Several algorithms have been suggested for minisatellite alignment. Their time complexity is high -- close to O(n^3) -- due to the necessary reconstruction of duplication histories. We investigate the uniqueness of optimal alignments computed under the common single-copy duplication model. To this extent, it is necessary to avoid ambiguity in the algorithm employed. We re-code the ARLEM algorithm in the form of a grammar, and apply a disambiguation technique which uses a mapping to a canonical representation of minisatellite alignments. Having arrived at a non-ambiguous algorithm this way, we demonstrate that the underlying model -- independent of the algorithm -- gives rise to an exorbitant number of different, co-optimal alignments when applied to real-world data. We conclude that alignment-free methods should be considered for minisatellite comparison.

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Benedikt Löwes and Robert Giegerich. Avoiding Ambiguity and Assessing Uniqueness in Minisatellite Alignment. In German Conference on Bioinformatics 2013. Open Access Series in Informatics (OASIcs), Volume 34, pp. 110-124, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2013)

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@InProceedings{lowes_et_al:OASIcs.GCB.2013.110,
  author =	{L\"{o}wes, Benedikt and Giegerich, Robert},
  title =	{{Avoiding Ambiguity and Assessing Uniqueness in Minisatellite Alignment}},
  booktitle =	{German Conference on Bioinformatics 2013},
  pages =	{110--124},
  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.2013.110},
  URN =		{urn:nbn:de:0030-drops-42285},
  doi =		{10.4230/OASIcs.GCB.2013.110},
  annote =	{Keywords: minisatellite alignment, dynamic programming, ambiguity}
}

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Avoiding Ambiguity and Assessing Uniqueness in Minisatellite Alignment

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