Hypergraph Covering Problems Motivated by Genome Assembly Questions
We describe some genome assembly problems as a general problem of covering a hypergraph by linear and circular walks, where vertices represent sequence elements, repeated sequences are modelled by assigning a multiplicity to vertices, and edges represent co-localization information. We show that deciding if a given assembly hypergraph admits an assembly is fixed-parameter tractable, and we provide two exact polynomial time algorithms for clearing ambiguities caused by repeats.
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- 3.Chauve, C., Patterson, M., Rajaraman, A.: Hypergraph covering problems motivated by genome assembly questions. arXiv:1306.4353 [cs.DS] (2013)Google Scholar
- 5.Manuch, J., Patterson, M., Wittler, R., Chauve, C., Tannier, E.: Linearization of ancestral multichromosomal genomes. BMC Bioinformatics 13(suppl. 19), S11 (2012)Google Scholar