细菌基因组岛相关模块的挖掘与分析

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1、上海交通大学硕士学位论文DATAMININGFORBACTERIALGENOMICISLAND-RELATEDMODULESABSTRACTBacteriapossessplasticgenomes,andgenomicislandisoneofthekeyfactorsdrivingtheevolutionofthegeneticvariety.Thisstudyemployedthemetholodogiesoftextminingandcomparativegenomicstoinvestigatebacterialgenomicislandsa

2、ndrelatedorassociatedgeneticmodules/factors,includingbacterialtypeIVsecretionsystems(T4SSs),non-codingRNA(ncRNA)genesandduplicatedgenes.Theweb-basedtoolmGenomeSubtractorforparallelinsilicosubtractivehybridizationanalysisofmultiplebacterialgenomes,couldidentifyputativegenomicisla

3、ndsbylocatingthevariableregionofthegenome.Toenhanceitsprocessingcapabilityandstability,computerprogramsweremodified.Datamanagementandretrievalmethodswereimprovedtoavoiddataredundancyandfacilitatedataupdateandmaintenance.Taskmanagementstrategywasdevelopedusingajobschedulingsystem

4、toorganizemultipletasks.Inaddition,keyparametersofmpiBLAST,therate-limitingstep,wereoptimized,whichdramaticallyimprovedtheefficiency.Meanwhile,thelocaldatabasecontainingthefullysequencedbacterialgenomeswasupdatedwith2078morerepliconsbeingavailableinthedrop-downmenuforanalysis.Mo

5、reover,wedevelopedafunctionalanalysismoduleforpartiallysequencedgenomes.IV万方数据上海交通大学硕士学位论文SomebacterialgenomicislandsuseT4SSsforconjugation.Wecollected10752corecomponentsmappingto811T4SSsand1884T4SSeffectorsfoundinrepresentativesof289bacterialspecieswith925directlyrelatedreferen

6、ces.WeimprovedtheT4SSsclassificationschemeandfurtherclassifiedidentifiedT4SSs.TherearetwoputativeT4SSsinKlebsiellapneumoniaeHS11286chromosomeandoneinaplasmidwithnoeffectordetected,andtheirfuctionsaretobefurtherstudied.TherearencRNAgeneslocatedinthecontextofsomegenomicislandsofba

7、cterialgenomesasgenomicislandsprefertoinsertattRNAandtmRNAgenes.Inthisstudy,weassessthreencRNAgene-predictiontoolsusedfrequentlyforthedifferentbacterialgenomes.ThesRNAPredicthadhigherspecificityandpositivepredictionvalue,butlowersensitivitythanPORTRAIT.Theperformanceofbothtoolsv

8、ariedwiththeselectedstrainsofdifferentG+Cconten