UC San Diego

The Genome Halving Problem is motivated by the whole genome duplication events in molecular evolution that double the gene content of a genome and result in a perfect duplicated genome that contains two identical copies of each chromosome. The genome then becomes a subject to rearrangements resulting in some rearranged duplicated genome. The Genome Halving Problem (first introduced and solved by Nadia El-Mabrouk and David Sankoff) is to reconstruct the ancestral pre-duplicated genome from the rearranged duplicated genome. The El-Mabrouk-Sankoff algorithm is rather complex and in this paper we present a simpler algorithm that is based on a generalization of the notion of the breakpoint graph to the case of duplicated genomes. This generalization makes the El-Mabrouk-Sankoff result more transparent and promises to be useful in future studies of genome duplications.