BGI 动物案例研讨班课件：5-Genome_Annotation.pdf

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1、GenomeAnnotationContents1.Tandemrepeatandtransposon2.Genestructureprediction3.Genefunctioninferring4.Non-codingRNAgene5.Regulatoryelement6.Datadisplayandpublish1.Tandemrepeatandtransposon•Tandemrepeats(satellite)Copy2Copy1Copy3•Dispersedrepeats(transposons)Copy1Copy2Co

2、py3TandemrepeatsClassifybasedonunitsize:•Satellite(unit>100bp)•Minisatellite(10bp

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