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MosaicSolver : a tool for determining recombinants of viral genomes from pileup data
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Wood, Graham, Ryabov, Eugene V., Fannon, Jessica, Moore, Jonathan D., Evans, David J. and Burroughs, Nigel John (2014) MosaicSolver : a tool for determining recombinants of viral genomes from pileup data. Nucleic Acids Research, Volume 42 (Number 16). Article number e123. doi:10.1093/nar/gku524 ISSN 0305-1048.
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Official URL: http://dx.doi.org/10.1093/nar/gku524
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.
| Item Type: | Journal Article | ||||||||
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| Subjects: | R Medicine > RA Public aspects of medicine | ||||||||
| Divisions: | Faculty of Science, Engineering and Medicine > Science > Life Sciences (2010- ) Faculty of Science, Engineering and Medicine > Research Centres > Warwick Systems Biology Centre |
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| Library of Congress Subject Headings (LCSH): | Virus diseases | ||||||||
| Journal or Publication Title: | Nucleic Acids Research | ||||||||
| Publisher: | Oxford University Press | ||||||||
| ISSN: | 0305-1048 | ||||||||
| Official Date: | 12 August 2014 | ||||||||
| Dates: |
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| Volume: | Volume 42 | ||||||||
| Number: | Number 16 | ||||||||
| Number of Pages: | 13 | ||||||||
| Article Number: | Article number e123 | ||||||||
| DOI: | 10.1093/nar/gku524 | ||||||||
| Status: | Peer Reviewed | ||||||||
| Publication Status: | Published | ||||||||
| Access rights to Published version: | Open Access (Creative Commons) | ||||||||
| Date of first compliant deposit: | 28 December 2015 | ||||||||
| Date of first compliant Open Access: | 28 December 2015 | ||||||||
| Funder: | Biotechnology and Biological Sciences Research Council (Great Britain) (BBSRC), Great Britain. Department for Environment, Food and Rural Affairs (DEFRA), Natural Environment Research Council (Great Britain) (NERC), Scotland. Scottish Government, Wellcome Trust (London, England), University of Warwick | ||||||||
| Grant number: | BBI0008281 (BBSRC) |
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