Genome Rearrangement by Reversals and Insertions/Deletions of Contiguous Segments

Analysis of genome rearrangements allows to compare molecular data from species that diverged a very long time ago. Results and complexities are tightly related to the type of data and genome-level mutations considered. For sorted and signed data, Hannenhalli and Pevzner (HP) developed the rst polynomial algorithm in the eld. This algorithm solves the problem of sorting by reversals. In this paper, we show how to extend the HP approach to include insertions and deletions, allowing to compare genomes containing diierent genes. We provide an exact algorithm for the asymmetric case, as applies in organellar genome evolution, and a heuristic for the symmetric case, with bounds and a diagnostic for determining whether the output is optimal.