關(guān)于多序列比對和系統(tǒng)發(fā)育分析中的序列空位研究.pdf

1、中國農(nóng)業(yè)大學(xué)碩士學(xué)位論文關(guān)于多序列比對和系統(tǒng)發(fā)育分析中的序列空位研究姓名：史衛(wèi)峰申請學(xué)位級別：碩士專業(yè)：昆蟲學(xué)指導(dǎo)教師：沈佐銳黃大衛(wèi)20050601AbstractlⅡ曲epastfewyearsmoreandmoremoleculardataisusedinentomologicalphylogenyanalysisMultiplesequencealignmentisthebasisofphylogeneticanalysisand

2、molecularsequencesarealignedviainsertinggapsAffinegappenaltyschemeiswidelyusedtoconstrainthenumberofgapsinordertogainameaningfulalignmentHoweverthegappenaltycostisarbitrarilydesignatedinthismethodPreviousresearchshowstha

3、tdifferentgappenaltiesmayberesultindifferentalignmentsHerewegivestatisticalevidenceoftheeffectsofgapsonmultiplesequencealignmentandillustratesomeotherstatisticalfeaturesofgapsWbdownloadedthirtyeightdatamatricesfromGenBan

4、kanddividedthemintofourkindsofmatrixtypes，rDNA—basedmatrices，exonDNAmatrices，exonAAmatricesandITSbasedmatricesThenweperformalignmentusingcomputerprogramClustalXl81whilesettingdifferentgappenaltieseachtimeforeverydatamatr

5、ixrespectivelyStatisticalresultsprovethatgapopeningandextensionpenaltiessignificantlychangethepercentageofthegapsPosthoetestsindicatethatq=4，r=1啪representcasesallowingmoregapsandg=15，r=8canrepresentcasesinsertingfewergap

6、sDifferentmatrixtypeshavesignificantlydifferentpercentagesofgapsCurvesconcerningpercentagesofoverallgapstogappenaltiescanbegeneralizedintothreetypesempiricallytheundeecurvethehorizontallineandthestepdowncIⅡveDifferentmat

7、rixtypeshavedifferentinclinationstokindsofcurvesExonAAmatricesaremoreconservativetb卸theirDNAmatricosAlthougbgappenaltiesaffecttheresultsofmultiplesequencealignment，itisnotclearwhetherthereisdifferenceamongresultsgotwhenu

8、singdifferentgapcodingmethodandfleesearchmethodAlignmentresultsgotbyusingq=4，r=1andq=15，r=8weIcselectedtoperformreconstructionReconstructionmethodincludesmaximumparsimony(MP)andBayesianInMPmethod，gapsarecodedasmissingdat

9、athefifthcharacterandtreatedbysimpleindelcodingmethodrespectivelyResIIltsofMPanalysisshowtllatchangesoftreelengthandnumberofinformativesitesa聆n’tsamewitheachotherwhengappenaltieschange7nledecreaseofgapsleadstothedecrease

10、ofCIandtheincreaseofHIThususingarelativelysmallgappenaltyallowinginsertingmoregapsisoftennecessaryGappenaltieshaveliuleeffectonbootstrapsupportvalues，howevertheychangethetopologicals橢ctoreandresolutionofstrictcoosensus1I

11、cesinmostCasesCodinggapsasfifthcharactercanincreasethenumberofinformativesitesandtreelengthcomparedwithcodinggapsasmissingdata，nevertheless，thenumberofⅧtreesdoasn’tdecreaseFurthermore，thesetwocodingmethodsdon’tsignifican

12、tlychangeCI，RI，RCandbootstrapsupportvaluesOnthecontrarythetopologicalstructmeandresolutionofstrictCOnSansustreesarenotsamemostlyCLRIandRChavesignificantdifferenceamongmatrixtypesSimpleindelcodingismoreefficientthancoding

13、gapsasmissingdataComparedwithcodinggapsasfifthcharactersimpleiodelcodingdocsn’tchangetheresultssignificantlyexceptthetopologicalstmctoreandresolutionofstrictconseRsustreesandbootstrapsupportValUesSimpleindelcodingplaysad

14、ifferentroleonthephylogenetieresultswhenpercentageofgapsisdifferentBayesiananalysisrevealsthatBPPshavenosignificantdifferencebetween50％consensustreesgotbyusingq=4，r=1andq215，r=8Likewise，onlyfewdatamatriceshavethesametopo

15、logicalStrUCtUreandresolutionof50％consensustreesInsumwedon’tbelieve蛐ylogeneticrelationshipacquiredbylimitedmolecularsequencesdataiscfedibleBycontraries，wethinksuchdiscrepsnciesofthetopologicalstructureandresolutionaremos

16、tprobabletohavebeenproducedintheprocessofalignmentSoteastermorebiologicalinformationtogetagoodalignmentresultratherthanthereconstructionmethodsmaybemoreimportanttoacorrectphylognneticresultKeywords：GapMultipleSequenceAli