title: MosaicSolver: a tool for determining recombinants of viral genomes from pileup data.
abstract: Viral recombination is a key evolutionary mechanism, aiding escape from host immunity, contributing to changes in tropism and possibly assisting transmission across species barriers. The ability to determine whether recombination has occurred and to locate associated specific recombination junctions is thus of major importance in understanding emerging diseases and pathogenesis. This paper describes a method for determining recombinant mosaics (and their proportions) originating from two parent genomes, using high-throughput sequence data. The method involves setting the problem geometrically and the use of appropriately constrained quadratic programming. Recombinants of the honeybee deformed wing virus and the Varroa destructor virus-1 are inferred to illustrate the method from both siRNAs and reads sampling the viral genome population (cDNA library); our results are confirmed experimentally. Matlab software (MosaicSolver) is available.
authors.affiliation: Warwick Systems Biology Centre, Senate House, University of Warwick, Coventry, CV4 7AL, UK g.r.wood@warwick.ac.uk.
authors.forename: Graham R
authors.initials: GR
authors.lastname: Wood
authors.affiliation: School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK.
authors.forename: Eugene V
authors.initials: EV
authors.lastname: Ryabov
authors.affiliation: School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK.
authors.forename: Jessica M
authors.initials: JM
authors.lastname: Fannon
authors.affiliation: Warwick Systems Biology Centre, Senate House, University of Warwick, Coventry, CV4 7AL, UK.
authors.forename: Jonathan D
authors.initials: JD
authors.lastname: Moore
authors.affiliation: School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK.
authors.forename: David J
authors.initials: DJ
authors.lastname: Evans
authors.affiliation: Warwick Systems Biology Centre, Senate House, University of Warwick, Coventry, CV4 7AL, UK.
authors.forename: Nigel
authors.initials: N
authors.lastname: Burroughs
mesh_terms: D000465:Algorithms; D016679:Genome, Viral; D059014:High-Throughput Nucleotide Sequencing; D034741:RNA, Small Interfering / Q000737:chemistry; D011995:Recombination, Genetic; D012984:Software
chemical_list: D034741:RNA, Small Interfering