UC San Diego

Abstract Background The introduction of the double cut and join operation (DCJ) caused a flurry of research into the study of multichromosomal rearrangements. However, little of this work has incorporated indels (i.e., insertions and deletions of chromosomes and chromosomal intervals) into the calculation of genomic distance functions, with the exception of Braga et al., who provided a linear time algorithm for the problem of DCJ-indel sorting. Although their algorithm only takes linear time, its derivation is lengthy and depends on a large number of possible cases. Results We note the simple idea that a deletion of a chromosomal interval can be viewed as a DCJ that creates a new circular chromosome. This framework will allow us to amortize indels as DCJs, which in turn permits the application of the classical breakpoint graph to obtain a simplified indel model that still solves the problem of DCJ-indel sorting in linear time via a more concise formulation that relies on the simpler problem of DCJ sorting. Furthermore, we can extend this result to fully characterize the solution space of DCJ-indel sorting. Conclusions Encoding indels as DCJ operations offers a new insight into why the problem of DCJ-indel sorting is not ultimately any more difficult than that of sorting by DCJs alone. There is still room for research in this area, most notably the problem of sorting when the cost of indels is allowed to vary with respect to the cost of a DCJ and we demand a minimum cost transformation of one genome into another.