注釋、進(jìn)化分析_第1頁
注釋、進(jìn)化分析_第2頁
注釋、進(jìn)化分析_第3頁
注釋、進(jìn)化分析_第4頁
注釋、進(jìn)化分析_第5頁
已閱讀5頁，還剩18頁未讀， 繼續(xù)免費(fèi)閱讀

下載本文檔

版權(quán)說明：本文檔由用戶提供并上傳，收益歸屬內(nèi)容提供方，若內(nèi)容存在侵權(quán)，請(qǐng)進(jìn)行舉報(bào)或認(rèn)領(lǐng)

文檔簡介

Genomeannotation&

evolutionanalysiswangwenliang@2011-03-31GenomeannotationEvolutionanalysisEvolutiontheoryRepeatGeneGenefunctionncRNARegulatoryelementComparativegenomicsPhylogeneticsanalysisPopulationgeneticsDarwinianandNeutraltheoryGenomeannotation TandemrepeatandtransposonGenestructurepredictionGenefunctioninferringNon-codingRNAgeneRegulatoryelementTandemrepeatandtransposonTandemrepeats(satellite)Dispersedrepeats(transposons)Copy1Copy2Copy3Copy1Copy2Copy3RepeatDenovoprediction1.structurecharacter 2.selfalignmentLib-basedalignment(repbase)Repeatmasker ProteinmaskExampleGeneExpressionmapping(blat)EST,cDNA,SAGE,tilingarray,solexatagsHomologybased(genewise,Ensembl)ProteinsofrelativespeciesKnownproteinsinSwissprotdatabaseDenovoprediction(HiddenMarkovModel)Fgenesh,Genescan,Augustus,SNAP(eukaryote)Glimmer,GenemarkS(prokaryote)IntegrateallgeneevidencesGenerateacombinedreferencegeneset:GLEANEstimateaccuracyanderrorratebyLatentClassAnalysis(LCA)ConstructconsensusgenemodelsbyDynamicProgramming(DP)EVMCalculateaccuracyweightsforeachevidencesComputeweightedconsensusgenestructuresGenefunctionalannotationGO(GeneOntology) ForeukaryotespeciesPANTHEROntology SimplifiedversionofGO.KO(KEGGOrthologySystem) ForbotheukaryoteandprokaryotespeciesCOG(ClustersofOrthologousGroupsofproteins) ForprokaryotespeciesNon-codingRNAgeneThenon-protein-codingRNAarealsocalledgenenow.Howmanytypes?Traditional:-tRNA,rRNARecentlydiscovered:-miRNA,snRNA,snoRNA,etc.Predictionmethod:blastagainsttemplate

sequence,becausetheyarehighlyconservedRegulatoryelementsPromoterpredictionTranscriptionalfactorbindingsites1.Comparativegenomics2.Phylogeneticsanalysis3.PopulationgeneticsEvolutionanalysis1.Comparativegenomics

HomologyHUMAN

CCAAGGTCACGACTACTCCAATTGTCACAACTGTTCCAACCGTCACGACTGTTGAACGCHIMPANZEE

CCAAGGTCACGACTACTCCAATTGTCACAACTGTTCCAACCGTCATGACTGTTGAACGGORILLA

CCAAGGTCACAACTACTCCAATTGTCACAACTGTTCCAACCGTCACGACTGTTGAACGGenefamilySpeciesGeneNumberSingle-copyorthologsMultiple-copyorthologsUniqueOtherorthologsCaprahircus235339301856522353Ovisaries2374194215617922464Bostaurus2089293218711519658Equuscaballus204199738164618719Canisfamiliaris192589551321818153Ailuropodamelanoleuca210019571396319842Homosapiens223899953482920531Musmusculus233179963920222080Rattusnorvegicus228419914719721606Syntenyandcolinearity2.Phylogeneticsanalysis18Process1)、Naturalselection

2)、Geneticdrift:inferthepreservationandchangesbymutation.Genomicsdrift:inferthepreservationandchangesbylarger-scalegenomecontents(genes,segmental,chromosomeandwholegenome)Twomaintopicsinevolutionaryinference:Patterns1)、Modesofdevelopment,hierarchiesofmorphologicalorientationandtheadaptivesignificanceofcolonyform2)、

Recognitionofspeciesandthetempoofspeciationandextinction3)、Macroevolutionarypatternsandtrends.Theparadigmofevolution:DarwinianandNeutral&nearlyneutraltheoryMotooKimuraTomokoOhtaFixationofmutationsThreetypesofselectionStatistic:Ka/Ks(dN/dS)

Definition:Ka:Theratioofthenumberofnonsynonymoussubstitutionspernonsynonymoussite.Ks:Theratioofthenumberofsynonymoussubstitutionspersynonymoussite.Function:1)、Diagnosingtheformofsequenceevolution.Ka/Ks<1,significantly:negativeselectionKa/Ks~1:neutralselectionKa/Ks>1,signific

溫馨提示

  • 1. 本站所有資源如無特殊說明，都需要本地電腦安裝OFFICE2007和PDF閱讀器。圖紙軟件為CAD,CAXA,PROE,UG,SolidWorks等.壓縮文件請(qǐng)下載最新的WinRAR軟件解壓。
  • 2. 本站的文檔不包含任何第三方提供的附件圖紙等，如果需要附件，請(qǐng)聯(lián)系上傳者。文件的所有權(quán)益歸上傳用戶所有。
  • 3. 本站RAR壓縮包中若帶圖紙，網(wǎng)頁內(nèi)容里面會(huì)有圖紙預(yù)覽，若沒有圖紙預(yù)覽就沒有圖紙。
  • 4. 未經(jīng)權(quán)益所有人同意不得將文件中的內(nèi)容挪作商業(yè)或盈利用途。
  • 5. 人人文庫網(wǎng)僅提供信息存儲(chǔ)空間，僅對(duì)用戶上傳內(nèi)容的表現(xiàn)方式做保護(hù)處理，對(duì)用戶上傳分享的文檔內(nèi)容本身不做任何修改或編輯，并不能對(duì)任何下載內(nèi)容負(fù)責(zé)。
  • 6. 下載文件中如有侵權(quán)或不適當(dāng)內(nèi)容，請(qǐng)與我們聯(lián)系，我們立即糾正。
  • 7. 本站不保證下載資源的準(zhǔn)確性、安全性和完整性, 同時(shí)也不承擔(dān)用戶因使用這些下載資源對(duì)自己和他人造成任何形式的傷害或損失。

最新文檔

評(píng)論

0/150

提交評(píng)論