Genomes of organisms undergo rearrangements and mutations over time, and genome evolutions are studied well by understanding this dynamism. Recombination, transposition and mutation are the three important processes that lead to these genomic changes. Genome rearrangements describe changes in the genetic linkage relationship of large chromosomal regions, involving reversals, transpositions, block interchanges, deletions, insertions, fissions, fusions and translocations etc. Many algorithms for calculating rearrangement scenarios between two genomes have been proposed. The calculated rearrangement scenario is often common for the same pair of permutations. Hence, deciding which calculated rearrangement scenario is more biologically meaningful is significant. Rearrangements have been shown to be responsible for numerous heritable diseases, evolution and specialization. The chromosomal regions affected by these rearrangements are called breakpoints, while those which have not been rearranged are called synteny blocks. To gain a better understanding of the evolutionary forces that affect genome architecture, Homologous synteny blocks (HSBs) and chromosome evolutionary breakpoint regions (EBRs) can be identified.
