Improved Approximation for Breakpoint Graph Decomposition and Sorting by Reversals

Sorting by Reversals (SBR) is one of the most widely studied models of genome rearrangements in computational molecular biology. At present, is the best known approximation ratio achievable in polynomial time for SBR. A very closely related problem, called Breakpoint Graph Decomposition (BGD), calls for a largest collection of edge disjoint cycles in a suitably-defined graph. It has been shown that for almost all instances SBR is equivalent to BGD, in the sense that any solution of the latter corresponds to a solution of the former having the same value. In this paper, we show how to improve the approximation ratio achievable in polynomial time for BGD, from the previously known to for any > 0. Combined with the results in (Caprara, Journal of Combinatorial Optimization, vol. 3, pp. 149–182, 1999b), this yields the same approximation guarantee for n! – O((n – 5)!) out of the n! instances of SBR on permutations with n elements. Our result uses the best known approximation algorithms for Stable Set on graphs with maximum degree 4 as well as for Set Packing where the maximum size of a set is 6. Any improvement in the ratio achieved by these approximation algorithms will yield an automatic improvement of our result.