大规模基因组测序中的信息分析课件

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。

SequenceDataDistributionVectorSequencingandDataProcessingProcedureBasecallingRepeatMarkORFPredictionGeneAnnotationFinishingAssembleVectorMarkPhredPhd2fastaCrossmatchPhrapConsedRepeatmaskerGlimmerBlastxBlastnClastaltRNAscanQualityControlQualCalQualDrawQualStatCOGsSwiss-port,PIR,GDB,GenBankSequencingNeuralnetworkmethod

Aimprovedback-propagation(BP)learningalgorithmhavebeenbuiltinthestudy.Onegoalofthisnetworkistofindthesplicingsitebetweenintronandexon.NeuralNetworkProcedurexl-1yW=synapticweightvectorofaneuroninlayerl

=thresholdofaneuroninlayerlV=vectorofnetinternalactivitylevelsofneuronsY=vectoroffunctionsignalsofneuronsinlayerl

(l)(l)(l)(l)

ForwardComputationinputvectorxdesiredresponsevextordThenetinternalactivitylevelforneuronjinlayerlisIfneuronjisintheoutputlayer(i.e.,l=L),setHence,computetheerrorsignal

BackwardComputationvectoroflocalgradientsofneuronsinlayerle=errorvectorrespresentedbye,e,….,easelements12qforneuronjinoutputlayerLforneuronjinhiddenlayerl

IterationFractaldimensionofexonandintron

Weintroducethemappingfromnucleotidesequencestotwo-dimensionalmetricspacebyassigningeachnucleotideafixedvectorandconstructingarepresentationbyjoiningthesevectorsend-to-end.FractalDimensionofExonandIntronSequencesDisthefractaldimensionandthereexistsself-similarityinthisrangeofthenucleotidesequence.--------------CGCGGCGTGTGTTATA--------------00.511.522.533.507654321IntronSeq.ExonSeq.RandomSeq.End-to-endRangeMainRangeGeometricRangelnNandareaverageofandofeachclassofsequences,andaretheirstandarddeviations.TheclassofexonsequencesisdenotedasEX,andintronsequencesIN,randomizedexonsequencesRE,andrandomizedintronsequencesRI.RelativeComplexityinExon,IntronandFlanks

Usingthemethodsandtechniquesincryptology

OnecouldthinkthattheDNAsequencesaresimilarwiththetelegram,whichhasbeenusedtotransmitsecretsinthefieldofcommerceormilitaryaffairs,sowetrytoapplymethodsandtechniquesincryptologytoDNAsequenceanalysis.

AsthefirststepweintroducesomeparametersofcryptologytoDNAsequenceanalysis.Coincidentindex

Incryptologythisparameterhasbeenusedtofindtheplaincodeinanencipheredtextofatelegram.Thepartwiththeplaincodeisthehigh-valueregionofthisparameter.Weassumethatexoniscorrespondingtotheplaincodeandalsohasthehigh-valueofthecoincidentindex.

UnicitydistanceTheValuesofCoincidentIndexinHSHSC70SequenceORFPredictionoftheContigby5MethodCompositeArtificialNeuralNetworkSystemA.

T.

tengcongensis

CompleteGenomeAnalysisThebacteriawasdesignatedasThermoanaerobactertengcongensisMB4whichwasisolatedfromthehotspringinTengcongarea,YunnanProvinceofChina,bythescientistsworkingintheinstituteofmicrobiologyofChineseAcademyofSciencesfouryearsago.Thecellmorphologyofthebacteriaisbaculiform,Gramreactionisnegative(-),itcannotformsporeandalsocannotmobilize.Thebacteriaisanaerobestooxygentolerance,optimumtemperatureis75oC,optimumpH7.0.ThegenomeofT.tengcongensis

consistsofasinglecircularchromosomeo