1and2-0805 for student

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1、XiuliLuLiaoninguniversitylxlbioinformatics@yahoo.cnbasedonSectionED.R.Westhead,BioinformaticsSearchingSequenceDatabasesby  SequenceSimilarityCriteriaMotivationFromwherearewe?RecentAfricavs.Multi-regionalHypotheseIn1999EncephalitiscausedbytheWestNileVirusbr

2、okeoutinNewYork.HowdidtheviruscometoNewYork?Howdidthenucleusgetintotheeucaryoticcells?ToanswersuchquestionswewillneedsequencecomparisonandphylogenetictreesE:SearchingSequenceDatabasesby  SequenceSimilarityCriteriaE1.SequencesimilaritysearchesE2.Aminoacidsu

3、bstitutionmatricesE3.Databasesearches:FASTAandBLASTHomologySimilaritybetweenspecies，sequencesthatshareacommonancestor,mayormaynothavesimilarfunctionBeforeDarwin,basedonmorphology–Similarbonesinbat’swingandwhale’sflipperDarwin’sevolutionarytheory–Commonance

4、stryGeneticsequences–EvolutionmadevisibleEvolutionarybasisofalignment(I)SequencealignmentsWhatareyoucomparing?HomologoussequencesOrthology:describesgenesindifferentspeciesthatderivefromacommonancestor.Orthologousgenesmayormaynothavethesamefunction.Paralogy

5、:describeshomologousgeneswithinasinglespeciesthatdivergedbygeneduplication.Evolutionarybasisofalignment(I)Similarityvs.HomologyAnysequencecanbesimilarSequenceshomologuesifevolvedfromcommonancestorAssumption:SimilarityindicatorforhomologyEnabletheresearcher

6、todetermineiftwosequencesdisplaysufficientsimilaritytojustifytheinferenceofhomology.SequenceSimilaritySearchesHomologyMotivationStudyevolution–ComparedifferentspeciesDiscoverfunction–CompareagainstknownspeciesFindcrucialfeatures–ComparemanyexamplesIdentify

7、causeofdisease–CompareagainsthealthyindividualsHomologyviaSequencesStudyevolution–MultiplealignmentandphylogenetictreesDiscoverfunction–BLASTsearchesagainstdatabaseFindcrucialfeatures–MotiffindingIdentifycauseofdisease–DetectvariablesitesinalignmentE1:Sequ

8、enceSimilaritySearchesE11.SequencesimilaritysearchesE12.SequencealignmentE13.AlignmentalgorithmsE14.AlignmentscoresandgappenaltiesE15.MeasurementofsequencesimilarityE11:SequenceSimilaritySearches（序列相似性检索）Sequ