Abstract

Abstract. Gene rearrangements have successfully been used in phylogenetic reconstruction and comparative genomics, but usually under the assumption that all genomes have the same gene content and that no gene is duplicated. While these assumptions allow one to work with organellar genomes, they are too restrictive when comparing nuclear genomes. The main challenge is how to deal with gene families, specifically, how to identify orthologs. While searching for orthologies is a common task in computational biology, it is usually done using sequence data. We approach that problem using gene rearrangement data, provide an optimization framework in which to phrase the problem, and present some preliminary theoretical results. 1

Citations