A new linear time algorithm to compute the genomic distance via the double cut and join distance

The genomic distance problem in the Hannenhalli-Pevzner (HP) theory is the following: Given two genomes whose chromosomes are linear, calculate the minimum number of translocations, fusions, fissions and inversions that transform one genome into the other. This paper presents a new distance formula based on a simple tree structure that captures all the delicate features of this problem in a unifying way, and a linear time algorithm for computing this distance. (C) 2009 Elsevier B.V. All rights reserved.