序列相似性搜索課件

第六章序列相似性搜索一、序列相似性搜索的任務(wù)和目的序列相似性搜索的任務(wù)序列相似性搜索的目的二、同源和相似三、序列的BLAST分析四、專門的BLAST服務(wù)器第六章序列相似性搜索1.序列比較的任務(wù)：發(fā)現(xiàn)序列之間的相似性辨別序列之間的差異2.目的：

相似序列相似的結(jié)構(gòu)，相似的功能判別序列之間的同源性推測序列之間的進(jìn)化關(guān)系一、序列相似性搜索的任務(wù)和目的1.序列比較的任務(wù)：一、序列相似性搜索的任務(wù)和目的1.同源（homology）-具有共同的祖先直向同源（Orthologous）共生同源（paralogous）2.相似（similarity）

同源序列一般是相似的 相似序列不一定是同源的

二、同源和相似一般認(rèn)為，蛋白質(zhì)序列間至少有80個(gè)氨基酸左右的區(qū)域有25%或更高的同源性；DNA序列具有75%以上的同源性有潛在的生物學(xué)意義。1.同源（homology）-具有共同的祖先二、同源和相三、序列的BLAST分析三、序列的BLAST分析BLAST(BasicLocalAlignmentSearchTool)allowsrapidsequencecomparisonofaquerysequenceagainstadatabase.TheBLASTalgorithmisfast,accurate,andweb-accessible.基本局域聯(lián)配搜尋工具BLASTBLAST(BasicLocalAlignmentSWebsiteofBLAST/BLAST/(BLAST2.0)http://www2.ebi.ac.uk/blast2/(WU-Blast2)/(WU-Blast2)WebsiteofBLASTWhyuseBLAST?BLASTsearchingisfundamentaltounderstandingtherelatednessofanyfavoritequerysequencetootherknownproteinsorDNAsequences.Applicationsinclude

identifyingorthologsandparalogsdiscoveringnewgenesorproteinsdiscoveringvariantsofgenesorproteinsinvestigatingexpressedsequencetags(ESTs)exploringproteinstructureandfunctionWhyuseBLAST?BLASTsearchingFourcomponentstoaBLASTsearch(1)Choosethesequence(query)(2)SelecttheBLASTprogram(3)Choosethedatabasetosearch(4)ChooseoptionalparametersThenclick“BLAST”FourcomponentstoaBLASTsea序列相似性搜索ppt課件序列相似性搜索ppt課件Step1:ChooseyoursequenceSequencecanbeinputinFASTAformat,plaintextformatorasaccessionnumberStep1:ChooseyoursequenceSeExampleoftheFASTAformatforaBLASTqueryExampleoftheFASTAformatfoStep2:ChoosetheBLASTprogramStep2:ChoosetheBLASTprogrStep2:ChoosetheBLASTprogramblastn(nucleotideBLAST)blastp(proteinBLAST)blastx(translatedBLAST)tblastn(translatedBLAST)tblastx(translatedBLAST)Step2:ChoosetheBLASTprogrChoosetheBLASTprogramProgram

Input

Database 1blastn

DNA

DNA 1blastp

protein

protein 6blastx

DNA

protein 6tblastn

protein

DNA 36tblastx

DNA

DNAChoosetheBLASTprogramPrograDNApotentiallyencodessixproteins5’CATCAA5’ATCAAC5’TCAACT5’GTGGGT5’TGGGTA5’GGGTAG5’CATCAACTACAACTCCAAAGACACCCTTACACATCAACAAACCTACCCAC3’3’GTAGTTGATGTTGAGGTTTCTGTGGGAATGTGTAGTTGTTTGGATGGGTG5’DNApotentiallyencodessixprStep3:choosethedatabasenr=non-redundant(mostgeneraldatabase)dbest=databaseofexpressedsequencetagsdbsts=databaseofsequencetagsitesgss=genomicsurveysequenceshtgs=highthroughputgenomicsequenceStep3:choosethedatabasenrStep4a:SelectoptionalsearchparametersCDsearchStep4a:SelectoptionalsearcBLASTNsearchingBLASTNsearchingStep4a:SelectoptionalsearchparametersEntrez!FilterExpectWordsizeorganism增加該值可提高查詢速度Step4a:SelectoptionalsearcBLAST:optionalparametersYoucan...?choosetheorganismtosearch?turnfilteringon/off?changetheexpect(e)value?changethewordsize?changetheoutputformatBLAST:optionalparametersYoufilteringfiltering序列相似性搜索ppt課件序列相似性搜索ppt課件Step4b:optionalformattingparametersAlignmentviewDescriptionsAlignmentsStep4b:optionalformattingp序列相似性搜索ppt課件taxonomydatabasequeryprogramtaxonomydatabasequeryprogramtaxonomytaxonomy序列相似性搜索ppt課件序列相似性搜索ppt課件BLASTformatoptionsBLASTformatoptionsBLASTformatoptions:multiplesequencealignmentBLASTformatoptions:multiple序列相似性搜索ppt課件thresholdscore=11EVDparametersBLOSUMmatrixEffectivesearchspace=mn=lengthofqueryxdblength10.0istheEvaluegappenaltiescut-offparametersWewillgettothebottomofaBLASTsearchinafewminutes…thresholdscore=11EVDparameBLASTPSearchingwithamultidomainprotein,polBLASTPSearchingwithamultid序列相似性搜索ppt課件SearchingbacterialsequenceswithpolSea