License: Creative Commons Attribution 3.0 Unported license (CC BY 3.0)
When quoting this document, please refer to the following
DOI: 10.4230/OASIcs.GCB.2013.14
URN: urn:nbn:de:0030-drops-42354
URL: http://dagstuhl.sunsite.rwth-aachen.de/volltexte/2013/4235/
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Bernt, Matthias ; Wieseke, Nicolas ; Middendorf, Martin

On Weighting Schemes for Gene Order Analysis

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Abstract

Gene order analysis aims at extracting phylogenetic information from the comparison of the order and orientation of the genes on the genomes of different species. This can be achieved by computing parsimonious rearrangement scenarios, i.e. to determine a sequence of rearrangements events that transforms one given gene order into another such that the sum of weights of the included rearrangement events is minimal. In this sequence only certain types of rearrangements, given by the rearrangement model, are admissible and weights are assigned with respect to the rearrangement type. The choice of a suitable rearrangement model and corresponding weights for the included rearrangement types is important for the meaningful reconstruction. So far the analysis of weighting schemes for gene order analysis has not been considered sufficiently. In this paper weighting schemes for gene order analysis are considered for two
rearrangement models: 1) inversions, transpositions, and inverse
transpositions; 2) inversions, block interchanges, and inverse transpositions. For both rearrangement models we determined properties of the weighting functions that exclude certain types of rearrangements from parsimonious rearrangement scenarios.

BibTeX - Entry

@InProceedings{bernt_et_al:OASIcs:2013:4235,
  author =	{Matthias Bernt and Nicolas Wieseke and Martin Middendorf},
  title =	{{On Weighting Schemes for Gene Order Analysis}},
  booktitle =	{German Conference on Bioinformatics 2013},
  pages =	{14--23},
  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 =		{http://drops.dagstuhl.de/opus/volltexte/2013/4235},
  URN =		{urn:nbn:de:0030-drops-42354},
  doi =		{10.4230/OASIcs.GCB.2013.14},
  annote =	{Keywords: Gene order analysis, maximum parsimony, weighting}
}

Keywords: Gene order analysis, maximum parsimony, weighting
Collection: German Conference on Bioinformatics 2013
Issue Date: 2013
Date of publication: 09.09.2013

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