geneious-软件使用手册-分子生物学

ResearchinaflashResearchinaflashGeneious4.8QuickstartManualBiomattersLtdMarch4,20102IntroductionThisquickstartmanualwillguideyouthroughthefeaturesofGeneious4.8’sinterfaceandhelpyouorientyourself.YoushouldalsotrytheGeneiousbuiltininteractivetutorialwhichcanbefoundbyselecting“Help”→“Tutorial”fromthemenu.Formoreinformationyoucangotofindanumberoftutorialsonmorespecifictopics.UserInterfaceOverviewFigure1:ThemainwindowinGeneiousOntheleftofFigure1arethesourcesandservicesinthe“SourcesPanel”.HereyoucanaccessmanyonlinedatabasesincludingNCBIandUniProt,thensimplydraganddropsequencesandotherdatatoyourLocalfolderswhereyoucanstore,viewandanalysetheminacustomisableworkspace.Rightclicking(CTRL+clickonMacOSX)ontheLocalfoldersallowsyoutocreatenewfolders,sharethemwithotherusers,delete,renameormovethem.Youcanalsomarkthecontentsasreadandexportanentirefolderincludingsubfoldersinasingleoperation.3Selectingadatasourcedisplaysthecontentsofthatsourceinthe“DocumentTable”.Thistablealwayshascolumnsrelevanttothetypeofdatayouareworkingwithmakingiteasytosortandlocatetheitemsyouarelookingfor.Clickontheheaderofacolumntosortorclickanddragtheheaderstoreorderthem.Rightclick(CTRL+clickonMacOSX)ontheheadertochangethecolumnsthatarevisible.Youcansortsequencesbylengthororganismforexample.Usethefilterboxabovethetabletoquicklylocateitemsbykeywordorclickthesearchbuttontoaccesspowerfulsearchingfunctionality.Selectinganiteminthetablegivesyouaviewofthedatainthe“DocumentView”areabelow.Geneiousalwayschoosesviewswhichareappropriateforthedatayouhaveselected.Oftenthereareseveralofthesesoyoucanswitchbetweenthemusingthetabsdirectlyabove.Apairwisealignmenthasanalignmentviewandadotplotforexample.The“HelpPanel”showscontextspecificinformationabouttheparticularviewerthatisinuse.ItalsoincludesthebuiltintutorialwhichcoversthemajorfunctionsofGeneiousPro.Ifyouneedsomeextraspacetoworkin,justclickthe“Expand”buttontoexpandthevieworthe“Open”buttontoopenitinaseparatewindow.Youcanalsoopenadocumentinanewwindowbydouble-clickingonitinthedocumenttable.ToaccessanyoftheanalysisfeaturesinGeneioussuchasBLASTsearching,sequencealign-mentandcloningjustselectthedatayouwanttoanalysebeforechoosingtheappropriateanalysisfromthetoolbarormenu.SequenceViewerBasicsThesequenceviewerallowsyoutodisplayyourannotatedsequenceoralignment.Theplusandminusbuttonsincreaseanddecreasethemagnificationofthesequence.Youcanzoominfullytoviewthebases/residues,andouttoseeanoverviewofthesequence(s).Zoomingcanalsobequicklyachievedbyholdingdownthezoommodifierkey(theAltkeyonWindows,LinuxandMacOSX)andclicking.Whenthezoomkeyispressedamagnifyingglassmousecursorwillbedisplayed.Thecolorsoptioncontrolsthecoloringofthesequencenucleotidesoraminoacids.Color-ingschemesdifferdependingonthetypeofsequence.Forexample,the“Polarity”and“Hy-drophobicity”coloringschemesareavailableonlyforProteinsequences.Annotationscanbeshownandhiddenbyopeningthe“Annotations”sectionofthesequenceviewerpanelandclickingthecheckboxnexttoeachannotationtype(Figure2).Byselectingaregionandclicking“Annotation”,acustomannotationcanbeaddedtoaregionofinterest.JustenteranameandclickOK.Annotationscanalsobecopiedbetweensequencesbyright-clicking(CTRL+clickonMacOSX)ontheannotation.4Figure2:AviewofanannotatednucleotidesequenceinGeneiousDatabasesGeneiousallowsyoutosearchfordocumentswithinyourlocalfolderswithease.Clickingthe“Search”buttonatthetoprightofthemainwindowwhenafolderisselectedwillallowyoutofinddocumentsbytextorsequence(Figure3).Selectthetop“Local”folderandclickSearchtosearchallofyourlocalfolders.Figure3:SearchingthelocalfoldersGeneiousProintegratescloselywithmanyonlinedatabasesincludingalargenumberfromNCBIsuchasNucleotide,Gene,SNP,PubMedandTaxonomyaswellasUniProtandPFam.Tosearchanyofthesetext-baseddatabases,selectthedatabaseinthesourcespanelthenyoucanperformasimplekeywordsearchbyenteringyourkeyword(s)intothesearchboxand5clickingthe“Search”button.Tosearchusingamorecomplexcombinationofterms,clickthe“MoreOptions”buttontotheright.(Figure4).Figure4:SearchingthePubMeddatabaseTheresultsofyoursearcharedisplayedastheyaredownloadedfromtheinternet.Whilethisishappeningyoucansortbyanyofthecolumnsorfiltertofindkeywordslikeaparticularcountryorspecies.Selectingdata,immediatelygivesyouagraphicalrepresentationofresultswithouthavingtonavigateawayfromthesearch.Whenyou’vefoundwhatyou’relookingforsaveitbyclickinganddraggingthedocument(s)fromthedocumenttableovertothedesiredfolderinthesourcespanel.SequenceSearchGeneiousProalsofeaturesintegratedaccesstoNCBI’sBLASTdatabasesandtheabilitytosetupyourownlocalpersonaldatabasesusingCustomBLAST.Tosearchforsimilarsequencesinanyofthesedatabases,firstselectyourquerysequence(orseveralforabatchsearch)thenclickonthe“SequenceSearch”button.Theoptionsthataredisplayedallowyoutochoosethedatabaseandparametersforyoursearch.6Onceyouclickthesearchbutton,Geneiouscreatesafolderfortheresultsandstartsdownload-ingthemwhenthesearchiscomplete(Figure5).Yourresultsaresavedstraightawaysoyouwon’tlosethemevenifyouhavetoclosetheprogram.Figu