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COMPUTER SCIENCE COLLOQUIUM

Inferring Genome Rearrangements in a Phylogenetic Tree

Matthias Bernt
Department of Mathematics and Computer Science
University of Leipzig, Germany

Tuesday, 12 August, 2008 at 14:15
IMADA's Seminar Room

ABSTRACT

The order of the genes on the chromosomes of species can be used for inferring their phylogenetic relationship. The inference of the rearrangements that formed the gene orders of today's species and the ancestral arrangement of the genes are problems arising in this field. We present here new approaches for these problems.

The CREx method (common interval rearrangement explorer) computes heuristically pairwise rearrangement scenarios for gene order data. CREx detects 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. As phylogenetic events in such scenarios reversals, transpositions, reverse transpositions, and tandem duplication random loss (TDRL) operations are considered. This makes it well suited for studying the gene order of mitochondrial genomes.

Based on CREx a method called TreeREx (tree rearrangement explorer) is proposed for solving the problem of finding a plausible and parsimonious assignment of genomic rearrangement events to the edges of a given phylogenetic tree. TreeREx 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 TreeREx can automatically infer the events and the ancestral gene orders for realistic biological examples of mitochondrial gene orders.

Host: Daniel Merkle


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