A Branch-and-Bound Method for the Multichromosomal Reversal Median Problem

Authors:
Meng Zhang;William Arndt;Jijun Tang
Affiliations:
College of Computer Science and Technology, Jilin University, China;Department of Computer Science and Engineering, University of South Carolina, USA;Department of Computer Science and Engineering, University of South Carolina, USA
Venue:
WABI '08 Proceedings of the 8th international workshop on Algorithms in Bioinformatics
Year:
2008

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Abstract

The ordering of genes in a genome can be changed through rearrangement events such as reversals, transpositions and translocations. Since these rearrangements are "rare events", they can be used to infer deep evolutionary histories. One important problem in rearrangement analysis is to find the median genome of three given genomes that minimizes the sum of the pairwise genomic distance between it and the three others. To date, MGR is the most commonly used tool for multichromosomal genomes. However, experimental evidence indicates that it leads to worse trees than an optimal median-solver, at least on unichromosomal genomes. In this paper, we present a new branch-and-bound method that provides an exact solution to the multichromosomal reversal median problem. We develop tight lower bounds and improve the enumeration procedure such that the search can be performed efficiently. Our extensive experiments on simulated datasets show that this median solver is efficient, has speed comparable to MGR, and is more accurate when genomes become distant.