Algorithms for Finding Gene Clusters
WABI '01 Proceedings of the First International Workshop on Algorithms in Bioinformatics
INFORMS Journal on Computing
On the tandem duplication-random loss model of genome rearrangement
SODA '06 Proceedings of the seventeenth annual ACM-SIAM symposium on Discrete algorithm
Perfect Sorting by Reversals Is Not Always Difficult
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Bioinformatics
Journal of Computer and System Sciences
Recovering true rearrangement events on phylogenetic trees
RECOMB-CG'07 Proceedings of the 2007 international conference on Comparative genomics
Computing common intervals of K permutations, with applications to modular decomposition of graphs
ESA'05 Proceedings of the 13th annual European conference on Algorithms
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Given the mitochondrial gene orders and the phylogenetic relationship of a set of unichromosomal taxa, we study the problem of finding a plausible and parsimonious assignment of genomic rearrangement events to the edges of the given phylogenetic tree. An algorithm called algorithm TreeREx(tree rearrangement explorer) is proposed for solving this problem heuristically. TreeRExis based on an extended version of algorithm CREx(common interval rearrangement explorer, [4]) that heuristically computes pairwise rearrangement scenarios for gene order data. As phylogenetic events in such scenarios reversals, transpositions, reverse transpositions, and tandem duplication random loss (TDRL) operations are considered. CRExcan detect such events as patterns in the signed strong interval tree, a data structure representing gene groups that appear consecutively in a set of two gene orders. TreeRExthen tries to assign events to the edges of the phylogenetic tree, such that the pairwise scenarios are reflected on the paths of the tree. It is shown that TreeRExcan automatically infer the events and the ancestral gene orders for realistic biological examples of mitochondrial gene orders. In an analysis of gene order data for teleosts, algorithm TreeRExis able to identify a yet undocumented TDRL towards species Bregmaceros nectabanus.