大规模基因组测序中的信息分析

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1、大规模基因组测序中的信息分析--拼接与注释大规模测序是基因组研究的最基本任务，它的每一个环节都与信息分析紧密相关。从测序仪的光密度采样与分析、碱基读出、载体标识与去除、拼接与组装、填补序列间隙、到重复序列标识、读框预测和基因标注的每一步都是紧密依赖基因组信息学的软件和数据库的。SequenceDataDistributionVectorSequencingandDataProcessingProcedureBasecallingRepeatMarkORFPredictionGeneAnnotationFinishingAssembleVectorMarkPhredPhd2f

2、astaCrossmatchPhrapConsedRepeatmaskerGlimmerBlastxBlastnClastaltRNAscanQualityControlQualCalQualDrawQualStatCOGsSwiss-port,PIR,GDB,GenBankSequencingHowtofindthecodingregionsinrudeDNAsequence?StatisticalmethodandSequenceAlignmentMethodenevenpositionalbasefrequence(Dvalue)Neuralnetworkpredi

3、ctingthesplicingsitesFractaldimensionofexonsandintronsComplexityanalysisHowmanydifferentpatternsarethereintheareaofthedifferentDNAsequence?MethodandTechniquesinCryptologyCoincidentIndexsUnicityDistance＃Hidden-Markovmethod(HMM)Glimmerv------NeuralnetworkmethodAimprovedback-propagation(BP)le

4、arningalgorithmhavebeenbuiltinthestudy.Onegoalofthisnetworkistofindthesplicingsitebetweenintronandexon.NeuralNetworkProcedurexl-1yW=synapticweightvectorofaneuroninlayerl=thresholdofaneuroninlayerlV=vectorofnetinternalactivitylevelsofneuronsY=vectoroffunctionsignalsofneuronsinlayerl(l)(l)(

5、l)(l)ForwardComputationinputvectorxdesiredresponsevextordThenetinternalactivitylevelforneuronjinlayerlisIfneuronjisintheoutputlayer(i.e.,l=L),setHence,computetheerrorsignalBackwardComputationvectoroflocalgradientsofneuronsinlayerle=errorvectorrespresentedbye,e,….,easelements12qforneur

6、onjinoutputlayerLforneuronjinhiddenlayerlIteration-------------GU-----------------AG-------------splicingsitesexonexonintronpseudosplicingsites---------------GU------------------AG--------------successrate=38/60~64%FractaldimensionofexonandintronWeintroducethemappingfromnucleotidesequen

7、cestotwo-dimensionalmetricspacebyassigningeachnucleotideafixedvectorandconstructingarepresentationbyjoiningthesevectorsend-to-end.FractalDimensionofExonandIntronSequencesDisthefractaldimensionandthereexistsself-similarityinthisrangeofthenucleotidesequence.----