Algorithms with restrictive input constrains on genome exemplar distance caculation

Abstract

The comparative study of gene order rearrangements has been restricted to the case when the genes in one genome are homologous to at most one gene in the other genome. Sankoff (1999) proposes the estimation of true exemplars, a selection of one gene from each gene family in both genomes such that the distance between the resulting exemplar strings is minimized, which is called exemplar distance. David Bryant in his paper show that the calculation of the exemplar distance between two genomes is NP-hard for both the signed reversals distance and the breakpoint distance, even with quite restrictive conditions on the input. Limite the input according to strictive conditions used by David Bryants' proof, here we provides two algorithm to solve problem under some input conditions. one is branch and bound algorithms ,the other is Greedy Algorithm for both distances .different DATA can use different Algorithm to get better performance. © 2012 Springer-Verlag GmbH.