ReAS Recovery of Ancestral Sequences for Transposable Elements from the Unassembled Reads of a Whole Genome Shotgun 英文参考文献.docVIP

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ReAS Recovery of Ancestral Sequences for Transposable Elements from the Unassembled Reads of a Whole Genome Shotgun 英文参考文献.doc

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ReAS Recovery of Ancestral Sequences for Transposable Elements from the Unassembled Reads of a Whole Genome Shotgun 英文参考文献

ReAS:RecoveryofAncestralSequencesfor TransposableElementsfromtheUnassembled ReadsofaWholeGenomeShotgun Ruiqiang Li1,2[,Jia Ye1,2[,Songgang Li2,3[,Jing Wang2[,Yujun Han2,Chen Ye2,Jian Wang1,2,Huanming Yang1,2 Jun Yu1,2,Gane Ka-Shu Wong1,2,4*,Jun Wang1,2,5,6* , 1JamesD.WatsonInstituteofGenomeSciencesofZhejiangUniversity,Hangzhou,China,2BeijingInstituteofGenomicsofChineseAcademyofSciences,BeijingGenomics Institute, Beijing, China, 3 College of Life Sciences, Peking University, Beijing, China, 4 UW Genome Center, Department of Medicine, University of Washington, Seattle, Washington,UnitedStatesofAmerica,5TheInstituteofHumanGenetics,UniversityofAarhus,Aarhus,Denmark,6DepartmentofBiochemistryandMolecularBiology, UniversityofSouthernDenmark,OdenseM,Denmark Wedescribeanalgorithm,ReAS,torecoverancestralsequencesfortransposableelements(TEs)fromtheunassembled readsofawholegenomeshotgun.ThemainassumptionsarethattheseTEsmustexistathighcopynumbersacross thegenomeandmustnotbesooldthattheyarenolongerrecognizableincomparisontotheirancestralsequences. Tested on the japonica rice genome, ReAS was able to reconstruct all of the high copy sequences in the Repbase repositoryofknownTEs,andincreasetheeffectivenessofRepeatMaskerinidentifyingTEsfromgenomesequences. Citation: LiR, Ye J,LiS,Wang J,HanY, et al(2005)ReAS:Recovery ofancestral sequences for transposableelements fromthe unassembledreads ofawholegenome shotgun.PLoSComputBiol1(4):e43. preferred by RepeatMasker, as divergence between an ancestral sequence and a present-day copy is half of that Introduction Transposable elements (TEs) make up a signi?cant pro- portionofmanyeukaryoticgenomes,totalingalmost45%for human[1],and50%to80%forrice,maize,andwheat[2–4]. They play important evolutionary roles [5,6], and can be essentialtoolsforgenomeanalyses[7].RepeatMasker(A.Smit andP.Green,unpublisheddata)isoneofthemostcommonly usedalgorithmsfordetectingTEs.Itreliesonacomparison to known TEs from libraries like Repbase [8], which rep