An Evolutionary Model-Based Algorithm for Accurate Phylogenetic Breakpoint Mapping and Subtype Prediction in HIV-1 英文参考文献.docVIP

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An Evolutionary Model-Based Algorithm for Accurate Phylogenetic Breakpoint Mapping and Subtype Prediction in HIV-1 英文参考文献.doc

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An Evolutionary Model-Based Algorithm for Accurate Phylogenetic Breakpoint Mapping and Subtype Prediction in HIV-1 英文参考文献

AnEvolutionaryModel-BasedAlgorithmforAccurate PhylogeneticBreakpointMappingandSubtype PredictioninHIV-1 SergeiL.KosakovskyPond1*,DavidPosada2,EricStawiski3,ColombeChappey3,ArtF.Y.Poon4 ,Gareth Hughes5,EstherFearnhill6,MikeB.Gravenor7,AndrewJ.LeighBrown8,SimonD.W.Frost4,9 1Department ofMedicine,UniversityofCalifornia SanDiego,LaJolla,California,UnitedStatesofAmerica,2DepartmentofBiochemistry,GeneticsandImmunology, UniversityofVigo,Vigo,Spain,3MonogramBiosciences,SouthSanFrancisco,California,UnitedStatesofAmerica,4DepartmentofPathology,UniversityofCaliforniaSan Diego,LaJolla,California, United States of America, 5Health Protection Agency East ofEngland Regional EpidemiologyUnit, Cambridge, United Kingdom, 6Medical ResearchCouncilClinicalTrialsUnit,London,UnitedKingdom,7SchoolofMedicine,UniversityofSwansea,Swansea,UnitedKingdom,8InstituteofEvolutionaryBiology, UniversityofEdinburgh,Edinburgh,UnitedKingdom,9DepartmentofVeterinaryMedicine,UniversityofCambridge,Cambridge,UnitedKingdom Abstract Genetically diverse pathogens (such as Human Immunodeficiency virus type 1, HIV-1) are frequently stratified into phylogenetically or immunologically defined subtypes for classification purposes. Computational identification of such subtypesishelpfulinsurveillance,epidemiologicalanalysisanddetectionofnovelvariants,e.g.,circulatingrecombinant forms in HIV-1. A number of conceptually and technically different techniques have been proposed for determining the subtype of a query sequence, but there is not a universally optimal approach. We present a model-based phylogenetic methodforautomaticallysubtypinganHIV-1(orotherviralorbacterial)sequence,mappingthelocationofbreakpointsand assigningparentalsequencesinrecombinantstrainsaswellascomputingconfidencelevelsfortheinferredquantities.Our Subtype Classification Using Evolutionary ALgorithms (SCUEAL) procedure is shown to perform very well in a variety of simulation scenarios, runs in parallel when multiple sequences are being screened,