Vector_NTI_Advance_11_Quick_Start_Guide

VectorNTIAdvance™11QuickStartGuideCatalogno.12605050,12605099,12605103Version11.0December15,2008126050222Publishedby:InvitrogenCorporation5791VanAllenWayCarlsbad,CA92008U.S.A.©2008InvitrogenCorporation.Allrightsreserved.ThisdocumentcontainsproprietaryinformationofInvitrogenCorporation.Nopartofthisdocument,includingdesign,coverdesign,andicons,maybereproducedortransmittedinanyform,byanymeans(electronic,photocopying,recording,orotherwise)withoutpriorwrittenagreementfromInvitrogenCorporation.Thesoftwaredescribedinthisdocumentisfurnishedunderalicenseagreement.InvitrogenCorporationanditslicensorsretainallownershiprightstothesoftwareprogramsofferedbyInvitrogenCorporationandrelateddocumentation.Useofthesoftwareandrelateddocumentationisgovernedbythelicenseagreementaccompanyingthesoftwareandapplicablecopyrightlaw.VectorNTIAdvanceandGatewayaretrademarksofInvitrogenCorporationintheUnitedStatesandothercountries.LogosofInvitrogenCorporationarealsotrademarksregisteredintheUnitedStatesandmayberegisteredinothercountries.Otherproductandbrandnamesaretrademarksoftheirrespectiveowners.GeneratedintheUnitedStates.InvitrogenCorporationreservestherighttomakeandhavemadechanges,withoutnotice,bothtothispublicationandtotheproductitdescribes.InformationconcerningproductsnotmanufacturedordistributedbyInvitrogenCorporationisprovidedwithoutwarrantyorrepresentationofanykind,andneitherInvitrogenCorporationnoritsaffiliateswillbeliableforanydamages.3TableofContentsIntroduction...........................................................................................................................................4OpeningVectorNTIAdvance™11.......................................................................................................5LocalDatabase.....................................................................................................................................6DatabaseBackup/Restore...................................................................................................................7MoleculeViewer....................................................................................................................................8SelectingandEditingMoleculeSequences......................................................................................9DesigningPCRPrimersfromaSequence.......................................................................................10CloneTwoFragmentswithClone2Seq............................................................................................11In-SilicoGeneSynthesiswithReGENerator....................................................................................12IdentifyingOpenReadingFrames(ORFs).......................................................................................13CreatingaRestrictionMap................................................................................................................14AligningMolecules.............................................................................................................................15ContigAssembly................................................................................................................................16AdditionalInformation.......................................................................................................................184IntroductionThisQuickStartGuideisdesignedtogetyoustartedusingVectorNTIAdvance™11.ItprovidesbriefdescriptionsoftheVectorNTIAdvance™11graphicaluserinterface,includingVectorNTIExplorerandtheMoleculeViewer,andstep-by-stepinstructionsforusingthemostcommonfeaturesandfunctionsofthesoftware.Thetopicscoveredincludelocatingthedesiredtools,displayingmolecules,designingPCRprimers,cloningtwofragments,genesynthesis,aligningmolecules,performingarestrictionanalysis,andassemblingcontigs.ThisguideassumesthatyouhaveaworkingknowledgeofbasicMicrosoft®Windows®andMacOS®featuresandfunctions(howtoopenandsavefiles,howtouseyourmouse,andsoon)andthatVectorNTIAdvance™11isinstalledonyourcomputer.5OpeningVectorNTIAdvance™11TheQuickStartPageisasinglepagethatconsolidatesmostcommonlyusedmodules,tools,andutilitiesthatVectorNTIAdvanceprovides.TolaunchtheQuickStartPage,selectStartAllProgramsInvitrogenVectorNTIAdvance11QuickStart.Figure1.QuickStartPageYoucanconfigurethesoftwaretoopenboththeMoleculeViewerandVectorNTIExplorerwhenyouselectVectorNTIfromtheStartmenu.1.IntheMoleculeViewerwindow,gototheEditmenuandselectOptions.2.IntheGeneraltabofthedialog,selecttheOpenLocalExplorerAtStartupcheckbox.3.ClickOKtomakethechange.6LocalDatabaseVectorNTIExploreristhemaintoolforaccessingtheinformationinyourlocalVectorNTIAdvance™database.UsingtheExplorer,youcanimport,open,export,andorganizemoleculesandotherdatabaseitems,andlaunchotherVectorNTIAdvance™modules(Figure2).TolaunchVectorNTIExplorer:•OnQuickStartPage,clickonLocalDatabase.•IntheMoleculeViewer,clickontheLocalDatabaseicon().•FromtheWindows®Startmenu,selectPrograms|Invitrogen|VectorNTIAdvance1