Heuristic algorithm for computing reversal distance with multigene families via binary integer programming

Hannenhalli and Pevzner developed the first polynomial-time algorithm for the combinatorial problem of sorting of signed genomic data. Their algorithm solves the minimum number of reversals required for rearranging a genome to another when gene duplication is nonexisting. In this paper, we show how to extend the Hannenhalli-Pevzner approach to genomes with multigene families. We propose a new heuristic algorithm to compute the reversal distance between two genomes with multigene families via the concept of binary integer programming without removing gene duplicates. The experimental results on simulated and real biological data demonstrate that the proposed algorithm is able to find the reversal distance accurately. ©2005 IEEE