MosaicSolver: A tool for determining recombinants of viral genomes from pileup data

Graham R. Wood; Eugene V. Ryabov; Jessica M 0 Fannon; Jonathan D. Moore; David J. Evans; Nigel Burroughs

doi:10.1093/nar/gku524

MosaicSolver: A tool for determining recombinants of viral genomes from pileup data

Graham R. Wood^*, Eugene V. Ryabov, Jessica M 0 Fannon, Jonathan D. Moore, David J. Evans, Nigel Burroughs

^*Corresponding author for this work

Research output: Contribution to journal › Article › peer-review

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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 themethod from both siRNAs and reads sampling the viral genome population (cDNA library); our results are confirmed experimentally. Matlab software (MosaicSolver) is available.

Original language	English
Article number	e123
Pages (from-to)	1-14
Number of pages	14
Journal	Nucleic Acids Research
Volume	42
Issue number	16
DOIs	https://doi.org/10.1093/nar/gku524
Publication status	Published - 15 Sept 2014

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Copyright the Author(s) 2014. Version archived for private and non-commercial use with the permission of the author/s and according to publisher conditions. For further rights please contact the publisher.

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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 themethod from both siRNAs and reads sampling the viral genome population (cDNA library); our results are confirmed experimentally. Matlab software (MosaicSolver) is available.",

author = "Wood, {Graham R.} and Ryabov, {Eugene V.} and Fannon, {Jessica M 0} and Moore, {Jonathan D.} and Evans, {David J.} and Nigel Burroughs",

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year = "2014",

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doi = "10.1093/nar/gku524",

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AU - Fannon, Jessica M 0

AU - Moore, Jonathan D.

AU - Evans, David J.

AU - Burroughs, Nigel

N1 - Copyright the Author(s) 2014. Version archived for private and non-commercial use with the permission of the author/s and according to publisher conditions. For further rights please contact the publisher.

PY - 2014/9/15

Y1 - 2014/9/15

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AB - 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 themethod from both siRNAs and reads sampling the viral genome population (cDNA library); our results are confirmed experimentally. Matlab software (MosaicSolver) is available.

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MosaicSolver: A tool for determining recombinants of viral genomes from pileup data

Abstract

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