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冠状病毒Coronavirusl论文-2005 Genomic Classification Using an Information-Based Similarity Index_ Application to the SARS Coronavirus.pdf

冠状病毒Coronavirusl论文-2005 Genomic Classification Using an Information-Based Similarity Index_ Application to the SARS Coronavirus.pdf

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时间：2020-03-16

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1、JOURNALOFCOMPUTATIONALBIOLOGYVolume12,Number8,2005©MaryAnnLiebert,Inc.Pp.11031116GenomicClassificationUsinganInformation-BasedSimilarityIndex:ApplicationtotheSARSCoronavirusALBERTC.-C.YANG,ARYL.GOLDBERGER,andC.-K.PENGABSTRACTMeasuresofgeneticdistancebasedonalignmentmethodsarecon

2、finedtostudyingsequencesthatareconservedandidentifiableinallorganismsunderstudy.Anumberofalignment-freetechniquesbasedoneitherstatisticallinguisticsorinformationtheoryhavebeendevelopedtoovercomethelimitationsofalignmentmethods.Wepresentanovelalignment-freeapproachtomeasuringthesi

3、milarityamonggeneticsequencesthatincorporateselementsfrombothwordrankorder-frequencystatisticsandinformationtheory.WefirstvalidatethismethodonthehumaninfluenzaAviralgenomesaswellasonthehumanmitochondrialDNAdatabase.WethenapplythemethodtostudytheoriginoftheSARScoronavirus.Wefindtha

4、tthemajorityoftheSARSgenomeismostcloselyrelatedtogroup1coronaviruses,withsmallerregionsofmatchestosequencesfromgroups2and3.Theinformationbasedsimilarityindexprovidesanewtooltomeasurethesimilaritybetweendatasetsbasedontheirinformationcontentandmayhaveawiderangeofapplicationsinth

5、elarge-scaleanalysisofgenomicdatabases.Keywords:Shannonentropy,SARScoronavirus.INTRODUCTIONGeneticdistancemeasuresareindicatorsofsimilarityamongspeciesorpopulationsandareusefulforreconstructingphylogeneticrelationships(GraurandLi,1999).Measuresofgeneticdistancearemainlyderivedf

6、romexaminingeachpairofsequencesalignednucleotide-by-nucleotideandestimatingthenumberofsubstitutions.Sincethemechanismofgenomeevolutionreliesnotonlyonpoint-mutationsbutrecombinationorhorizontalgenetransferfromotherspecies,theheterogeneityofgenesegmentswillsubstantiallydegradethe

7、accuracyofoptimalsequencealignmentmethods,whicharebasedontheestimationofnucleotidesubstitution.Therefore,alignmentmethodsareconfinedtostudyingsequencesthatareconservedandidentifiableinallorganismsunderstudy(VingaandAlmeida,2003).CardiovascularDivisionandMargretandH.A.ReyInstitute

8、forNonlinearDynamicsinMedicine,BethIsraelDeaconessMedi

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