On Weighting Schemes for Gene Order Analysis

Authors Matthias Bernt, Nicolas Wieseke, Martin Middendorf

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Matthias Bernt
Nicolas Wieseke
Martin Middendorf

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Matthias Bernt, Nicolas Wieseke, and Martin Middendorf. On Weighting Schemes for Gene Order Analysis. In German Conference on Bioinformatics 2013. Open Access Series in Informatics (OASIcs), Volume 34, pp. 14-23, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2013)


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.
  • Gene order analysis
  • maximum parsimony
  • weighting


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