Coordinates and intervals in graph-based reference genomes.

ABSTRACT:

Background

It has been proposed that future reference genomes should be graph structures in order to better represent the sequence diversity present in a species. However, there is currently no standard method to represent genomic intervals, such as the positions of genes or transcription factor binding sites, on graph-based reference genomes.

Results

We formalize offset-based coordinate systems on graph-based reference genomes and introduce methods for representing intervals on these reference structures. We show the advantage of our methods by representing genes on a graph-based representation of the newest assembly of the human genome (GRCh38) and its alternative loci for regions that are highly variable.

Conclusion

More complex reference genomes, containing altern

SUBMITTER: Rand KD 

PROVIDER: S-EPMC5437615 | biostudies-literature | 2017 May

REPOSITORIES: biostudies-literature