Journal
Publisher
SCITEPRESS
DOI: 10.5220/0010165400210029
Keywords
Pangenome; Coordinate System; Directed Acyclic Graph; Level Function; Minimum Path Cover
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Funding
- DFG [OH 53/7-1]
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The pan-genome defines the space for genomic analyses, with graphs being the most natural representation. The Computational Pan-Genomics Consortium identified desirable properties for graphical frameworks, such as spatiality, monotonicity, and readability, and introduced a coordinate system for DAGs based on the level function and minimum path cover.
The Computational Pan-Genomics Consortium (Consortium, 2016) described the role of coordinate systems in genomics as follows: A pan-genome defines the space in which (pan-)genomic analyses take place. It should provide a 'coordinate system' to unambiguously identify genetic loci and (potentially nested) genetic variants. The most natural representations of pangenomes are graphs. The Computational Pan-Genomics Consortium identified desirable properties of the linear reference genome model that graphical frameworks should attempt to preserve: spatiality, monotonicity, and readability. In this paper, we introduce a coordinate system for DAGs that has these properties. It is based on the level function and a minimum path cover of the graph. Moreover, we describe a new method for finding a minimum path cover in a DAG, which works very well in practice.
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