2026-07-26T04:38:50Z https://drops.dagstuhl.de/oai

oai:drops-oai.dagstuhl.de:4235 2024-03-06T10:29:22Z ddc:004 open_access

On Weighting Schemes for Gene Order Analysis Bernt, Matthias Wieseke, Nicolas Middendorf, Martin Gene order analysis maximum parsimony weighting 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. Schloss Dagstuhl – Leibniz-Zentrum für Informatik Matthias Bernt and Nicolas Wieseke and Martin Middendorf 2013 Is Part Of OASIcs, Volume 34, German Conference on Bioinformatics 2013 InProceedings Text doc-type:ResearchArticle publishedVersion application/pdf doi:10.4230/OASIcs.GCB.2013.14 urn:nbn:de:0030-drops-42354 https://drops.dagstuhl.de/entities/document/10.4230/OASIcs.GCB.2013.14 eng https://creativecommons.org/licenses/by/3.0/legalcode