Journal of Graph Algorithms and Applications
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Special Issue on Selected Papers from the Second International Workshop on Algorithms and Computation, WALCOM 2008
On the Approximability of Comparing Genomes with Duplicates
Vol. 13, no. 1, pp. 19-53, 2009. Regular paper.
Abstract A central problem in comparative genomics consists in computing a (dis-)similarity measure between two genomes, e.g. in order to construct a phylogenetic tree. A large number of such measures has been proposed in the recent past: number of reversals, number of breakpoints, number of common or conserved intervals etc. In their initial definitions, all these measures suppose that genomes contain no duplicates. However, we now know that genes can be duplicated within the same genome. One possible approach to overcome this difficulty is to establish a one-to-one correspondence (i.e. a matching) between genes of both genomes, where the correspondence is chosen in order to optimize the studied measure. Then, after a gene relabeling according to this matching and a deletion of the unmatched signed genes, two genomes without duplicates are obtained and the measure can be computed. In this paper, we are interested in three measures (number of breakpoints, number of common intervals and number of conserved intervals) and three models of matching (exemplar, intermediate and maximum matching models). We prove that, for each model and each measure M, computing a matching between two genomes that optimizes M is . We show that this result remains true even for two genomes G1 and G2 such that G1 contains no duplicates and no gene of G2 appears more than twice. Therefore, our results extend those of [,,]. Besides, in order to evaluate the possible existence of approximation algorithms concerning the number of breakpoints, we also study the complexity of the following decision problem: is there an exemplarization (resp. an intermediate matching, a maximum matching) that induces no breakpoint ? In particular, we extend a result of  by proving the problem to be in the exemplar model for a new class of instances, we note that the problems are equivalent in the intermediate and the exemplar models and we show that the problem is in in the maximum matching model. Finally, we focus on a fourth measure, closely related to the number of breakpoints: the number of adjacencies, for which we give several constant ratio approximation algorithms in the maximum matching model, in the case where genomes contain the same number of duplications of each gene. Keywords: genome rearrangements, , duplicate genes, breakpoints, adjacencies, common intervals, conserved intervals, approximation algorithms.
Submitted: January 2008.
Published: February 2008.
Reviewed: July 2008.
Revised: July 2008.
Accepted: November 2008.
Final: December 2008.
Communicated by Md. Saidur Rahman