Genomic Distance with DCJ and Indels

Abstract

The double cut and join (DCJ) operation, introduced by Yancopoulos, Attie and Friedberg in 2005, allows one to represent most rearrangement events in genomes. However, a DCJ cannot perform an insertion or a deletion and most approaches under this model consider only genomes with the same content and without duplications, including the linear time algorithms to compute the DCJ distance and to find an optimal DCJ sorting sequence. In this work, we compare two genomes with unequal content, but still without duplications, and present a new linear time algorithm to compute the genomic distance, considering DCJ and indel operations. With this method we find preliminary evidence of the occurrence of clusters of deletions in the Rickettsia bacterium.