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Coordinates and intervals in graph-based reference genomes.

Knut D Rand1, Ivar Grytten2, Alexander J Nederbragt2,3

  • 1Department of Mathematics, University of Oslo, Moltke Moes vei 35, Oslo, 0851, Norway. knutdr@math.uio.no.

BMC Bioinformatics
|May 20, 2017
PubMed
Summary
This summary is machine-generated.

Future reference genomes may use graph structures to capture species diversity. This study introduces a standard method for representing genomic intervals on these complex graph genomes, enabling better utilization of genomic data.

Keywords:
EpigenomicsPan-genomeReference genomeSequence graphs

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Area of Science:

  • Bioinformatics
  • Genomics
  • Computational Biology

Background:

  • Future reference genomes are proposed to be graph structures to better represent species sequence diversity.
  • A standardized method for representing genomic intervals on graph-based reference genomes is currently lacking.

Purpose of the Study:

  • To formalize offset-based coordinate systems for graph-based reference genomes.
  • To introduce methods for representing genomic intervals on graph structures.

Main Methods:

  • Formalization of offset-based coordinate systems.
  • Development of methods for interval representation on graph genomes.
  • Application to the human genome assembly (GRCh38) and its alternative loci.

Main Results:

  • Demonstrated the advantage of the proposed methods by representing genes on a graph-based human genome.
  • Successfully represented genes on GRCh38, including highly variable regions and alternative loci.

Conclusions:

  • Complex reference genomes necessitate methods for representing genomic data on alternative loci.
  • The proposed notation facilitates the full utilization of GRCh38 alternative loci and future graph genomes.
  • A Python package and interactive web tool have been developed to support these methods.