An O(N2) algorithm for signed translocation problem

Genome rearrangement is an important area in computational biology. There are three basic operations, reversal, translocation, and transposition. Here we study the translocation operations. Multichromosomal genomes frequently evolve by translocation events that exchange genetic material between two chromosomes. We focus on the signed case, where the direction of each gene is known. The signed translocation problem asks to find the minimum number of translocation operations as well as the sequence of translocation operations to transform one genome into the other. A lineartime algorithm that computes the the minimum number of translocation operations was given in Li et al., 2004. However, that algorithm cannot give the optimum sequence of translocation operations. The best known algorithm that can give the optimum sequence of translocation operations for signed translocation problem runs in time. In this paper, we design an algorithm.