On the Practical Solution of the Reversal Median Problem

Authors:
Alberto Caprara
Affiliations:
-
Venue:
WABI '01 Proceedings of the First International Workshop on Algorithms in Bioinformatics
Year:
2001

Citing 8
Cited 6

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Abstract

In this paper, we study the Reversal Median Problem (RMP), which arises in computational biology and is a basic model for the reconstruction of evolutionary trees. Given q genomes, RMP calls for another genome such that the sum of the reversal distances between this genome and the given ones is minimized. So far, the problem was considered too complex to derive mathematical models useful for its practical solution. We use the graph theoretic relaxation of RMP that we developed in a previous paper [6], essentially calling for a perfect matching in a graph that forms the maximum number of cycles jointly with q given perfect matchings, to design effective algorithms for its exact and heuristic solution. We report the solution of a few hundred instances associated with real-world genomes.