Improved bounds on sorting by length-weighted reversals

Abstract

We study the problem of sorting binary sequences and permutations by length-weighted reversals. We consider a wide class of cost functions, namely f ( ℓ ) = ℓ α for all α ⩾ 0 , where ℓ is the length of the reversed subsequence. We present tight or nearly tight upper and lower bounds on the worst-case cost of sorting by reversals. Then we develop algorithms to approximate the optimal cost to sort a given input. Furthermore, we give polynomial-time algorithms to determine the optimal reversal sequence for a restricted but interesting class of sequences and cost functions. Our results have direct application in computational biology to the field of comparative genomics.