NCBI-BLAST-官网使用教程

NCBIHandoutSeries|BLASThomepage&searchpages|LastUpdateMay8,2015Contact:[e-mail] BLASTHomepageandSelectedSearchPagesIntroducingtheBLASThomepageandformelements/functionsofselectedsearchpages•NationalLibraryofMedicine•NationalInstitutesofHealth•DepartmentofHealthandHumanServicesBackgroundBLAST[1]isasuiteofprogramsprovidedbyNCBIforaligningquerysequencesagainstthosepresentinaselectedtar-getdatabase.TheNCBIBLASThomepage()providesanaccesspointforthesetoolstoper-formsequencealignmentontheweb.TheBLASTHomepageTheBLASThomepageconsistsofseveralsections,eachprovidesaspecificsetoffunctions:1.Thecommonheader(A),presentinmostBLAST-relatedpages,provideseasyaccesstoothercontentorfunc-tionsnotdirectlyaccessiblefromthehomepage.2.Therighthandcolumn(B)provideslinkstoalistofrecentlycompletedresults,BLAST-relatednewsandsearchtips.3.PageswithwebformsforsubmittingsearchesarelistedaslinksinthebodyoftheBLASThomepage.Theselinksareorganizedintothreecatego-ries,“BLASTAssembledRefSeqGe-nomes”(C),“BasicBLAST”(D),and“SpecializedBLAST”(E).4.Thesearchbox(F)inthe“BLASTAssembledGenomes”sectiontakesthenameofanorganismasinputandsuggestsalistofcandidates.Select-ingfromthesuggestedlistwilllocatethebestgenomicsequencedatasetforBLASTalignmentpurposes.ThecommonBLASTheaderThecommonBLASTheaderprovidesaconvenientwaytonavigateamongdifferentpagestoaccessdifferentcontentsorfunctions.TheNCBIlogo(G)linkstotheNCBIhomepage()toallowaccesstonon-BLASTrelatedfunctionsandcontent.The“Home”tab(H)linkstotheBLASThomepage.BLASTsearchresultsaretemporarilysavedfor36hours.The“RecentResults”tab(I)linkstoapagethatkeepstrackofrecentlysubmittedsearchrequeststhathavenotexpired.TheRequestIDuniquelyassignedtoasubmittedsearchprovidesaone-clickaccesstothatresult.The“SavedStrategies”tab(J)listsasetofsearchsetupssavedearlier.Itallowstheexaminationofsearchsettingsused,quickre-launchofthesesearches,anddownloadofspecificstrategiesforsharingorre-useinstandaloneBLAST.The“Help”tab(K)pointstopagewithalistoflinkstohelpdocuments,tutorials,referencesandusefuldownloaddirectoriesontheBLASTftpsite.MyNCBI[2]isafreeaccountfromNCBI,whichallowsuserstocustomizetheirsitepreferenceandmanagetheirworksperformedontheNCBIsite.Login-relatedlinksforMyNCBI(L)areattheright.BLASTsearchesperformedwhileloggedintoaMyNCBIaccountenablesaccesstoBLASTsearchresultsfortheirfull36-hourlifespanthroughthe“RecentResults”tab.Strategiessavedwillbesavedpermanently.HLGJKICBDEAFPage2BLASThomepage&searchpagesContact:[e-mail]|BLASThomepage&searchpages|LastUpdateMay8,2015The“RecentResults”pageBLASTsearchresultsareavailablefor36hours.The“RecentResults”tabdisplaysalistofrecentlysubmittedsearchrequeststhathavenotexpired.Thelistissession-specificandwillbelostifsessioncookieiscleareduponbrowserexit.Forthisreason,itisrecommendedthatBLASTsearchesbedonewithanactivelogintoaMyNCBIaccountsuchastheoneshownbelow.TheMyNCBIloginfromtheheaderisshownasaninsertattheupperright(A).Eachresultisgivenasarowinthetable.TheidentifierintheRequestID(RID)column(B)providesanone-clickaccesstothesearchresult.Theprogram,TitleandDatabasecolumn(C)combinetoprovideasummaryforaspecificsearch.Databaserestrictionappliedareindicatedby“more…”andthepopupuponmouseover(D).The“save”,“download”andtheredx(E)allowsavingthesearchstrategy,downloadingthesearchstrategy,andremovingthesearchfromthelist.Theinputbox(F)abovethetableisforretrievingotherresultsusingtheirassignedRIDs,suchasthosesharedamongcolleagues,usedasteachingordemonstra-tionexamples,orthosewithissuesencounteredandreportedtoNCBI’sblast-helpgroup.Clickingthe“Go”buttonwithoutanRIDloadstheformatform(G)wherethecontent(H)andformat(I)ofresultscanbeadjusted.The“SavedStrategies”pageThe“SavedStrategies”tab(shownbelow)displaysalistofsearchstrategies.Thefirstfourcolumns(J)provideagoodsummaryofthesearchsettingsforeachsavedentry.The“view”link(K)loadsthesettingsinasearchpage,whilethe“download”link(L)savesthesettingsinanASN.1for-mattedfileforusewithstandaloneBLASTorreload-ingonthewebser-vicesusingthe“ChooseFile”and“View”button(M).ClickingtheredX(N)removestheentryfromthelist.FABCEJKLMNGIHDBLASThomepage&searchpagesPage3 NCBIHandoutSeries|BLASThomepage&searchpages|LastUpdateMay8,2015Contact:[e-mail] FunctionsofBLASTsearchpagesTherearefiveBLASTsearchpages,eachperformsaspecifictypeofsequencealignment.Thesepagesarethefounda-tionfortheNCBIBLASTserviceandwillbedescribedinmoredetail.Table1belowsummarizeskeyaspectsofpages.Thesepagesaccessasetofcommondatabases,asummaryofthecontentsforthesedatabasesaregiveninTable2.Search page Query & database  combinaon   Alignment type Programs & funcons  (default program in bold) nucleode blast nucleode  vs nucleode nucleode  vs   nucleode megablast: for sequence idenficaon, intra‐species comparison disconguous megablast: for cross‐species comparison, searching with coding sequences blastn: for searching w