Improving the Performance of a Genome Sorting Algorithm with Inverted Block-Interchange

A classic problem in comparative genomics is to find a shortest sequence of evolutionary operations that transform one genome into another. There are different types of genome rearrangement operators such as reversals, transpositions, translocations, block interchange, double cut and join (DCJ) etc. In this paper we consider reversals and block-interchanges simultaneously and incorporate inverted block-interchange in a heuristic algorithm, which inverts one or both of the two swapped segments of a block-interchange. Experimental results confirm that incorporation of inverted block-interchange always results in a better (or at least equal) sorting sequence.