An Overview of Genomic Distances Modeled with Indels

TLDR: A new graph structure is introduced that gives a unified view of classical and some extensions of the classical approaches to compute the genomic distance, present an overview of their results and point out some open problems related to them.

Abstract: The genomic distance typically describes the minimum number of large-scale mutations that transform one genome into another. Classical approaches to compute the genomic distance are usually limited to genomes with the same content and take into consideration only rearrangements that change the organization of the genome (i.e., positions and orientation of pieces of DNA, and number of chromosomes). In order to handle genomes with distinct contents, also insertions and deletions of pieces of DNA—named indels—must be allowed. Some extensions of the classical approaches lead to models that allow rearrangements and indels. In this work we introduce a new graph structure that gives a unified view of these approaches, present an overview of their results and point out some open problems related to them.