Schloss Dagstuhl - Leibniz-Zentrum fuer Informatik GmbH Schloss Dagstuhl - Leibniz-Zentrum fuer Informatik GmbH scholarly article en L÷wes, Benedikt; Giegerich, Robert License
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URN: urn:nbn:de:0030-drops-42285


Avoiding Ambiguity and Assessing Uniqueness in Minisatellite Alignment



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.

BibTeX - Entry

  author =	{Benedikt L{\"o}wes and Robert Giegerich},
  title =	{{Avoiding Ambiguity and Assessing Uniqueness in Minisatellite Alignment}},
  booktitle =	{German Conference on Bioinformatics 2013},
  pages =	{110--124},
  series =	{OpenAccess Series in Informatics (OASIcs)},
  ISBN =	{978-3-939897-59-0},
  ISSN =	{2190-6807},
  year =	{2013},
  volume =	{34},
  editor =	{Tim Bei{\ss}barth and Martin Kollmar and Andreas Leha and Burkhard Morgenstern and Anne-Kathrin Schultz and Stephan Waack and Edgar Wingender},
  publisher =	{Schloss Dagstuhl--Leibniz-Zentrum fuer Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{},
  URN =		{urn:nbn:de:0030-drops-42285},
  doi =		{10.4230/OASIcs.GCB.2013.110},
  annote =	{Keywords: minisatellite alignment, dynamic programming, ambiguity}

Keywords: minisatellite alignment, dynamic programming, ambiguity
Seminar: German Conference on Bioinformatics 2013
Issue date: 2013
Date of publication: 2013

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