Recently accepted for publication
Wood et al., (2014) MosaicSolver: a tool for determining recombinants of viral genomes from pileup data. Nucleic Acids Research (in press)
Viral recombination is a key evolutionary mechanism, aiding escape from host immunity, changes in tropism and possibly transmission across species barriers. Determining whether recombination has occurred and the specific recombination points 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, using siRNAs and sequence data sampling the viral genome population (cDNA library). Matlab software (MosaicSolver) is available.