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时间:2020-08-29
《BGI 动物案例研讨班课件:5-Genome_Annotation.pdf》由会员上传分享,免费在线阅读,更多相关内容在教育资源-天天文库。
1、GenomeAnnotationContents1.Tandemrepeatandtransposon2.Genestructureprediction3.Genefunctioninferring4.Non-codingRNAgene5.Regulatoryelement6.Datadisplayandpublish1.Tandemrepeatandtransposon•Tandemrepeats(satellite)Copy2Copy1Copy3•Dispersedrepeats(transposons)Copy1Copy2Co
2、py3TandemrepeatsClassifybasedonunitsize:•Satellite(unit>100bp)•Minisatellite(10bp3、ntermediate•ClassI:retrotransopons,copyandpasteincludeLTR,LINE,SINE,PLE,DIRS•ClassII:DNAtransposons•SubclassI:cutandpasteincludeTIRandCrypton•SubclassII:copyandpaste,rollingcycle,includeHelitronandMaverick.Reference:ThomasWicker,et.al.Aunifiedclassificationsystemforeuk4、aryotictransposableelements.2007.NatureReviewsGenetics.volume85、973HowtoannotateTEsTwosteps:•TEdiscovery–IdentificationofnewTEfamilies•Includeconsensussequenceandclassificationinformation–Constructionofaspecies-specificlibrary•TEdetection–IdentificationofindividualTEsfr6、ompreviouslydiscoveredTEfamiliesReference:CaseyM.BergmanandHadiQuesneville.Discoveringanddetectingtransposableelementsingenomesequences.2007.BIOINFORMATICS.VOL8.NO6.382-392MethodsofTEdiscovery•Denovopredictionmethods–Useintrinsicrepetition,withoutanypriorknowledgeabout7、TEs•Homology-basedmethods–RelyonhomologytoknownTEsequences(Repbase,TEproteinlibraryinRepeatMaskerpackage)•Structure-basedmethods–Baseonpriorknowledgeaboutthecommonstructuralfeatures(LTR_FINDER)•Comparativegenomicmethods–DetectnewTEsinmultiplesequencealignmentsDenovopre8、dictionsoftwareSoftwareInputStrategyRECONGenomeassemblyAlignmentPILERGenomeassemblyAlignmentRepeatScoutGenomeassemblyKmerRepeatModeler*GenomeassemblyAlignment+KmerReASSangerreadsKmer*RepeatModelerusesbothRECONandRepeatScoutascoresoftware,andissuitabletousedon>500Mbgeno9、mes.TheReASAlgorithmComparativegenomicmethodsAreplicationeventwiththeresultinginsertionregionandjuxtaposedgapsinthemu
3、ntermediate•ClassI:retrotransopons,copyandpasteincludeLTR,LINE,SINE,PLE,DIRS•ClassII:DNAtransposons•SubclassI:cutandpasteincludeTIRandCrypton•SubclassII:copyandpaste,rollingcycle,includeHelitronandMaverick.Reference:ThomasWicker,et.al.Aunifiedclassificationsystemforeuk
4、aryotictransposableelements.2007.NatureReviewsGenetics.volume8
5、973HowtoannotateTEsTwosteps:•TEdiscovery–IdentificationofnewTEfamilies•Includeconsensussequenceandclassificationinformation–Constructionofaspecies-specificlibrary•TEdetection–IdentificationofindividualTEsfr
6、ompreviouslydiscoveredTEfamiliesReference:CaseyM.BergmanandHadiQuesneville.Discoveringanddetectingtransposableelementsingenomesequences.2007.BIOINFORMATICS.VOL8.NO6.382-392MethodsofTEdiscovery•Denovopredictionmethods–Useintrinsicrepetition,withoutanypriorknowledgeabout
7、TEs•Homology-basedmethods–RelyonhomologytoknownTEsequences(Repbase,TEproteinlibraryinRepeatMaskerpackage)•Structure-basedmethods–Baseonpriorknowledgeaboutthecommonstructuralfeatures(LTR_FINDER)•Comparativegenomicmethods–DetectnewTEsinmultiplesequencealignmentsDenovopre
8、dictionsoftwareSoftwareInputStrategyRECONGenomeassemblyAlignmentPILERGenomeassemblyAlignmentRepeatScoutGenomeassemblyKmerRepeatModeler*GenomeassemblyAlignment+KmerReASSangerreadsKmer*RepeatModelerusesbothRECONandRepeatScoutascoresoftware,andissuitabletousedon>500Mbgeno
9、mes.TheReASAlgorithmComparativegenomicmethodsAreplicationeventwiththeresultinginsertionregionandjuxtaposedgapsinthemu
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