Mapping to a Reference Genome Structure
Continuing the discussion of papers related to graph based representation of reference genomes, we will read a technical paper this week on a new way to look at the structure of reference genomes. Note the time!
The paper is a preprint from arXiv, entitled Mapping to a Reference Genome Structure, by Benedict Paten, Adam Novak, and David Haussler. arXiv:1404.5010.
To support comparative genomics, population genetics, and medical genetics, we propose that a reference genome should come with a scheme for mapping each base in any DNA string to a position in that reference genome. We refer to a collection of one or more reference genomes and a scheme for mapping to their positions as a reference structure. Here we describe the desirable properties of reference structures and give examples. To account for natural genetic variation, we consider the more general case in which a reference genome is represented by a graph rather than a set of phased chromosomes; the latter is treated as a special case.