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A Column-Generation Based Branch-and-Bound Algorithm for Sorting By Reversals.pdf

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A Column-Generation Based Branch-and-Bound Algorithm for Sorting By Reversals

A COLUMN{GENERATION BASEDBRANCH{AND{BOUND ALGORITHMFOR SORTING BY REVERSALSAlberto Caprara, Giuseppe Lancia+ and See{Kiong Ngo DEIS, University of Bologna, Italy+ GSIA, Carnegie{Mellon University, USAo Computer Science Department, Carnegie{Mellon University, USAJuly 1995AbstractWe consider the problem of sorting a permutation by reversals (SBR), calling forthe minimum number of reversals transforming a given permutation of f1; : : : ; nginto the identity permutation. SBR was inspired by computational biology appli-cations, in particular genome rearrangement. We propose an exact branch-and-bound algorithm for SBR. A lower bound is computed by solving a linear programwith a possibly exponential (in n) number of variables, by using column generationtechniques. An eective branching scheme is described, which is combined witha greedy algorithm capable of producing near{optimal solutions. The algorithmpresented can solve to optimality SBR instances of considerably larger size withrespect to previous existing methods.1 IntroductionUntil recently, most evolutionary studies in molecular biology have been based on se-quence alignment, i.e. comparison of single genes to detect local mutations in the se-quence of nucleotides. However, in the last few years, we have witnessed an increasinginterest in analyzing entire genomes at once, this way shifting the attention from genelevel to chromosome level (Sanko et al., [13], Sanko, [12]). In fact, as it is oftenfound that the order of genes is preserved more easily than the DNA sequence (see [3],[14]), looking at genomes instead of DNA sequences allows one to build some otherwiseextremely dicult evolutionary scenarios; this is particularly true for plant mitochon-drial DNA, virology and Drosophila genetics. Rearrangement of genomes can occur inmany dierent ways, among which inversions, transpositions, deletions, insertions andduplications of fragments.Let the order of the genes in two single{chromosome organisms be given by pe