; TeX output 1993.01.20:1045/B3nOUcfmBK`yG cmr10BDoubleKDigesterManOual4K`yff cmr10Version1.1BetaߊkManualbyJohnReinitz,JueProgrambyLawrenceWrightVkW+XQ cmr12CenrterforMedicalInformaticsUMDYValeMedicalScrhoSol,333CedarSt.,NewHaven,CT06510USA*/B3nH"VG cmbx10HCon4tentsBE0N cmbx121GettingStarted_ߍ4UM1.1,JASimpleExampletԍ,g cmmi12: C:::::::::::::::::::::::::::::::{4,J1.1.1R?TheMainDDWindorw: C:::::::::::::::::::::::::{4,J1.1.2R?LoadingaFileҷ: C::::::::::::::::::::::::::::::{5,J1.1.3R?MakingaRestrictionMapič: C:::::::::::::::::::::::{5,J1.1.4R?TheImpSortanceofConstrainrtsxP: C::::::::::::::::::::{5,J1.1.5R?ExpSerimenrtalError鍑: C:::::::::::::::::::::::::::{6,J1.1.6R?AssertingConstrainrts؍: C::::::::::::::::::::::::::{6,J1.1.7R?SarvingtoaFileH: C:::::::::::::::::::::::::::::{61.2,JDataEnrtry6: C:::::::::::::::::::::::::::::::::::{7,J1.2.1R?GraphicalDataEnrtryA: C:::::::::::::::::::::::::{7,J1.2.2R?TrypinginVValues:ލ: C::::::::::::::::::::::::::::{71.3,JDoingMoreWithDD ): C:::::::::::::::::::::::::::::{8E2Referencep92.1,JSixMainWindorws@6: C:::::::::::::::::::::::::::::::{9,J2.1.1R?ButtonskB: C:::::::::::::::::::::::::::::::::{9R?2.1.1.1lxPropupMenus.: C::::::::::::::::::::::::102.2,JTheTVopWindorw: C::::::::::::::::::::::::::::::::10,J2.2.1R?Help: C:::::::::::::::::::::::::::::::::::10,J2.2.2R?Con gureÍ: C::::::::::::::::::::::::::::::::11R?2.2.2.1lxDisplaryinMonoSchrome/Color.: C:::::::::::::::11R?2.2.2.2lxSetDefaultDataDirectoryV.ZÍ: C:::::::::::::::::11R?2.2.2.3lxShorwDetailsofMapBuilding.;: C:::::::::::::::12,J2.2.3R?Exit: C:::::::::::::::::::::::::::::::::::122.3,JTheDigestDataWindorwa: C:::::::::::::::::::::::::::12,J2.3.1R?Digests: C::::::::::::::::::::::::::::::::::12R?2.3.1.1lxMethoSd1:8GraphicalInrterface.p: C:::::::::::::::13R?2.3.1.2lxMethoSd2:8TrypeinVValues.ꍑ: C:::::::::::::::::13R?2.3.1.3lxLoadedFilesandDoubleDigests.o^: C::::::::::::::14R?2.3.1.4lxOtherFilesinDataDirectoryV.+Ս: C::::::::::::::::14R?2.3.1.5lxSubSdirectoriesofDataDirectoryV.,*: C::::::::::::::1421ՠ/B3d/}h! cmsl12CONTENTSdd[cDDmanrualrrGnR?2.3.1.6lxMorveUpDirectoryTVree.6: C:::::::::::::::::::15UM,J2.3.2R?Sarve: C:::::::::::::::::::::::::::::::::::15R?2.3.2.1lxSarveDatainaNewFile. 7: C:::::::::::::::::::15R?2.3.2.2lxAppSendDatatoanExistingFile.: C::::::::::::::15R?2.3.2.3lxReplaceDatainanExistingFile.7捑: C::::::::::::::16,J2.3.3R?ErrorV: C:::::::::::::::::::::::::::::::::::16R?2.3.3.1lxChangeSize-EstimateErrorRanges.M: C::::::::::::16R?2.3.3.2lxChangeBasisofSizeComparisons.): C:::::::::::::16R?2.3.3.3lxUnseenFVragmenrts:8SizeCeiling. 0l: C::::::::::::::17R?2.3.3.4lxUnseenFVragmenrts:8NumbSerAllowedPerMatch.: C:::::17,J2.3.4R?Other&: C::::::::::::::::::::::::::::::::::17R?2.3.4.1lxChoSoseLaneStandard.󩍑: C:::::::::::::::::::17R?2.3.4.2lxDropLaneStandard.l: C:::::::::::::::::::::18R?2.3.4.3lxHide/ShorwLaneStandard.: C:::::::::::::::::18R?2.3.4.4lxCritiqueCurrenrtData.: C::::::::::::::::::::18R?2.3.4.5lxHide/ShorwSettings.F㍑: C:::::::::::::::::::::18R?2.3.4.6lxRenameDigest.\: C::::::::::::::::::::::::18R?2.3.4.7lxSetDNATrypSe.3: C::::::::::::::::::::::::19,J2.3.5R?Digest:8d": C:::::::::::::::::::::::::::::19,J2.3.6R?GelLaneTitle 02: C:::::::::::::::::::::::::::::19R?2.3.6.1�lxAddNewFVragmenrtsviaMouse.�鲍: C:::::::::::::::19R?2.3.6.2�lxAddNewFVragmenrtsviaKeybSoard.5: C:::::::::::::19R?2.3.6.3�lxChangeSize-EstimateErrorRanges.M: C::::::::::::20R?2.3.6.4�lxChangeEnzyme(orLaneStandard).: C::::::::::::20,J2.3.7R?BandonGel�X: C:::::::::::::::::::::::::::::::20R?2.3.7.1�lxAbSoutFVragmenrt<enzyme,size>.�Ķ: C::::::::::::::20R?2.3.7.2�lxAssertConstrainrt.͍: C::::::::::::::::::::::20R?2.3.7.3�lxIdenrtical.4: C:::::::::::::::::::::::::::20R?2.3.7.4�lxNotIdenrtical.Ѝ: C:::::::::::::::::::::::::20R?2.3.7.5�lxBiggerThan.: C:::::::::::::::::::::::::21R?2.3.7.6�lxSmallerThan.D̍: C:::::::::::::::::::::::::21R?2.3.7.7�lxConrtains(PartOf�8).: C:::::::::::::::::::::21R?2.3.7.8�lxNotConrtains(NotPartof�8).: C:::::::::::::::::21R?2.3.7.9�lxChangeSize-EstimateErrorRanges.M: C::::::::::::21R?2.3.7.10�lxChangeSizeData.: C::::::::::::::::::::::21R?2.3.7.11�lxRemorveFVragment. : C::::::::::::::::::::::212.4,JTheConstrainrtsWindow: C::::::::::::::::::::::::::::22,J2.4.1R?ConstrainrtsǍ: C:::::::::::::::::::::::::::::::22R?2.4.1.1�lxDrop.W: C:::::::::::::::::::::::::::::22R?2.4.1.2�lxNegate(Un-Negate).: C:::::::::::::::::::::22,J2.4.2R?Add h: C:::::::::::::::::::::::::::::::::::22R?2.4.2.1�lxIdenrtical.4: C:::::::::::::::::::::::::::222d�2�����������������������������������������!H/B3��dCONTENTSdd[cDDmanrualr�rGnR?2.4.2.2�lxNotIdenrtical.Ѝ: C:::::::::::::::::::::::::22UMR?2.4.2.3�lxBiggerThan.: C:::::::::::::::::::::::::23R?2.4.2.4�lxSmallerThan.D̍: C:::::::::::::::::::::::::23R?2.4.2.5�lxConrtains(PartOf�8).: C:::::::::::::::::::::23R?2.4.2.6�lxNotConrtains(NotPartof�8).: C:::::::::::::::::23,J2.4.3R?Dropp: C:::::::::::::::::::::::::::::::::::23,J2.4.4R?Negate: C::::::::::::::::::::::::::::::::::232.5,JMaps: C:::::::::::::::::::::::::::::::::::::::23,J2.5.1R?MakreMaps: C:::::::::::::::::::::::::::::::24R?2.5.1.1�lxNOTE,WARNINGorERRrORconcerningyourdata.: C::24R?2.5.1.2�lxWARNING:ThisloSokslikreahardproblem.z: C::::::::24,J2.5.2R?Con gureÍ: C::::::::::::::::::::::::::::::::24R?2.5.2.1�lxChangeMapDisplaryFVormat.F#: C::::::::::::::::24R?2.5.2.2�lxChangeMapFileOutputStryle.: C:::::::::::::::25R?2.5.2.3�lxAncrhoraDoubleDigestFVragmentinLeft/12-O'CloSckPosition.vd25,J2.5.3R?Sarve: C:::::::::::::::::::::::::::::::::::25R?2.5.3.1�lxChangeMapFileOutputStryle.: C:::::::::::::::25R?2.5.3.2�lxSarveAllMapstoFile.: C::::::::::::::::::::25R?2.5.3.3�lxSarveCurrentMaptoFile.䍑: C::::::::::::::::::262.6,JMatcrhDetailsm : C::::::::::::::::::::::::::::::::::26E3Installation�andIn�ternals ?273.1,JMacinrtoshP: C::::::::::::::::::::::::::::::::::::27,J3.1.1R?Installation|: C:::::::::::::::::::::::::::::::27,J3.1.2R?TVroubleshoSoting : C:::::::::::::::::::::::::::::283.2,JUnixandX11: C::::::::::::::::::::::::::::::::::28,J3.2.1R?Installation|: C:::::::::::::::::::::::::::::::28,J3.2.2R?TVroubleshoSoting : C:::::::::::::::::::::::::::::293.3,JAllVVersionsލ: C:::::::::::::::::::::::::::::::::::29,J3.3.1R?ErrorRecorvery#: C:::::::::::::::::::::::::::::29,J3.3.2R?MemoryManagemenrt: C::::::::::::::::::::::::::29,J3.3.3R?SarvingLargeMapFiles ȍ: C::::::::::::::::::::::::303.4,JFVurtherInformationandSuggestions�: C:::::::::::::::::::::302d�3�����������������������������������������IӠ/B3nHChapter 12��Getting Started8k͍Double Digester(DD)isaprogramdesignedtohelpyroumakerestrictionmapsfromgelUMdata.\YVou|givreitfragmentsizesfromtwodi erentsinglerestrictiondigeststogetherwiththeq<fragmenrtsfromthedoubledigestdonewithbSothenzymes.gDataentrycanbSedonewiththemouse,ϡthekreybSoardorfroma le.-Usingthemouseallowsyoutoworkdirectlyfromapictureofyrourgel.DDwrorksonaMacintosh,NandalsoonUnixusingtheXWindowSystem(X11).Withafewmsmallexceptions,լDDgbSeharvesmthesameonbothplatforms.0"ThismanrualisintendedforbSothplatforms.'Itassumesthatyrouknowthebasicsofstartinganapplicationundereithersystem.+Thismanrualhasthreechapters.+ThisintroSductorysectionisdesignedtoteachyoutheB%basicsofDDAasrapidlyandsmoSothlyaspossible.�Chapter2isareferencesection,cwhicrhdescribSesevrerythingthatDDcando.Chapter3tellsyouhowtoinstallDDonyoursystemandkreepitworking.(V<"V�G� ���cmbx101.1-CASimpleExampleӡStartKDD.OnaMacinrtosh,youKdothisbrydoubleclicking. \+UnderUnix/X11,justtypSe\1߆T� ��� ���cmtt12double-digester"afterthecommandpromptinaterminalemrulationwindow(donotrun_itinthebacrkground)./rAfterapause,theDDXwindowwillappSear./rYVoucanlearnaboutDDgbrygfmovingthepSointeraroundtheDDgwindow. FVorexample,ƖifthepSointerisoverthe^uwrord\Digests",{hamessageappSearsinthetopwindowthattellsyouthattheDigestscommandisusedto\enter,,loadorselectadoubledigestdataset"."ʫ7"V�ff� ���cmbx101.1.12TheMainDDWindo=wMThe.JmainwindorwofDD.isdividedintofourareas:ڱ\Digest,Data",S\Constraints",\Maps"and_anareaacrossthetopusedfordisplaryingmessages.rEacharea(window)hasamenubar.The\Digest,Data"windorwisforinputdata.5ItcontainsarepresentationofthedatathatloSokslikreagelonwhichthesedigestshavebSeenrun.DD'sresultswillbedisplaryedinthe\Maps"Pawindorw.sThe\Constraints"windowisusedtokeeptrackofadditionalinformation2�4�����������������������������������������j/B3��dCHAPTER1. #GETTINGSTVARTEDdd[cDDmanrualr�rGnabSoutNIyrourdata.Noticethe\Exit"onthetopmenubar:itwillgetyououtofDD.YVoucanUMalsoexitbryusingthenormalclose-bSox,menuorotheroptionsprovidedonyourcomputer."ʫ1.1.22LoadingaFileMTVoIseehorwDDworks,Mrclickonceontheword\Digests"inthe\Digest,Data"menubar.AԾmenruappSears.YVoucangetoutofthisoranryotherpSop-upmenubyclickingon\CANCEL".eThemenrucontainsalistofoptions,եincludinganindentedlistof lesthatstartsunder6theheading\Files,inDataDirectory".,TVry6clicrkingonpD4321,whichcontains(.@� ��� ���cmti12EcffoRI/HindISII)<andlDde�Idoubledigestdataforthatplasmid.c+AdialogbSorxwillappearpSoinrtingOoutthatyouareprobablyworkingwithcircularDNAOl(true,sincepD4321isaplasmid).DD%alwrays&BchecksyourdataforinternalconsistencybSeforemakingmaps(see2.3.4.4). SJust8clicrkon\OK",andadiagramofagelwillappSearinthe\Digest,Data"windorw.1.1.32MakingaRestrictionMapMClicrkonMake,Mapsinthe\Maps"window.=ArestrictionmapappSears,:inlinear,circularand95textform. $ThetextmapshorwsfragmentslabSeledbytheirsizes,withverticallinesforchcutsites.Thelinearandcircularmapseacrhhavethreelines,oneforeachdigest.ThedoubleGdigestisinthecenrter,^)andrestrictionsitesarelabSeledbyverticaltics.NNoticethatputtingʽthepSoinrteroverafragmentcausesinformationabSoutthatfragmenttoappSearinthewindorw.1FVorexample,ifyouputthepSointeroverthe1.12or0.67kbDdexfragments,DDwilltellyrouthattheyareunorderedwithinthe2.92kbE/H5fragment.1.1.42TheImpuortanceofConstrain=tsMNorwloSokatthe\Constraints"window.6ItsaysthattheDde�I1.12fragmentisidenticaltotheDde�I-E/HK1.12fragmenrt,andsimilarlyforthe0.67and0.47/0.45kbfragments.B$TheseconstrainrtsareimpSortantfactsabSoutyourdatathatcannotbSeeasilyexpressedintermsoffragmenrtsize.,OnmanygelsyoucantellbyinspSectionthatapairofbandsintwodi erentlanes$arethesamefragmenrt,ordi erentfragments.UImpSosingconstraintsishowyoutellDDabSoutimportanrtthingsthatyouknowabSoutyourdata.TVoseehorwimpSortantconstraintsare,*tryremovingthem.~Justclickon\Drop",*thenclicrk0ontheconstraint.dwYVoucanalsoclickdirectlyontheconstraint,andpick\Drop"fromtheBpSop-upmenru.�Afteryouhaveremovedallthreeconstraints,d@clickagainon\Make,Maps".WithUtheconstrainrtsDDfound1map,butnowithasfound11.Themapdisplayed tsthedatabSest,towithin2%oftheassignedfragmenrtsizes.%Themapsarelistedinorderof�goSodnessof t,andyroucanstepthroughthembyclickingon\Next"and\Prev"inthe\Maps"windorw.2d�5�����������������������������������������u3/B3��dCHAPTER1. #GETTINGSTVARTEDdd[cDDmanrualr�rGn1.1.52Expuerimen=talErrorMYVoucantellDDabSouttheaccuracyofyrourdataaswell.ELoSokatthetextrepresentationofUMmaph2ofthe11mapsyroujustmadebyremovingthethreeconstraints. ZNoticethatthe0.67kbDde�Ifragmenrtwasmatchedwiththe0.78kbE/H{Dde�Ifragment.:ThismeansthatDDtreatedthemasthesamefragmenrtbSecauseofexperimenrtaluncertaintyabSouttheirsize.YVouocanseewhrybyloSokingatthe\Digest,Data"window..xEachbandonthegelhaserrorbarsoneacrhsidewhichgraphicallyshowhowmuchuncertaintythereisabSoutthefragmentsizes.Theherrorbarsofthe0.67kbDde�Ihfragmenrtoverlapwiththeerrorbarsofthe0.78kbE/H{Dde�Ifragmenrt.:yWhenDD rstcomesup,theerrorbarsaresettoavreryroughestimateX4ofthereliabilitryofatypicalgel.YVoumayknowconsiderablymorethanthatabSoutthereliabilitryofyourdata,andyoucantellDDabSoutthataswell.YVoucancrhangeerrorrangesinavXarietyofways:`forthewholegel,forasinglelane,oronebandatatime.nInthisexample,"wre'lldoitforthewholegel.Clicrkon\Error"inthe\Digest,Data"+windorw.ApSopupmenuappSears.Clickon\Change,Size-EstimateErrorRanges,(defaultnow2.0StandardDeviations)".]Anotheri|pSopupmenruappearswitha crhoiceoferrorranges.YVoucanspSecifythemeitherasfragmentsizeerrorin%,maorasStandard`Deviation. SuppSoseforamomenrtthatyouhadrunthisgelverycarefullyV,andwrere Zquitecertainthatyourfragmentsizeswereaccurateto5%.qClickon5%inthe\GlobalError,Level"pSopup.8Norwclickon\Make,Maps"again.8YVouaredowntotwomaps."ʫ1.1.62AssertingConstrain=tsThereare2mapsbSecauseDDdoesnotknorwwhetherthe0.47E/H:fragmentmatchesthe0.45 E/H{Dde�I fragmenrtorthe0.35kbE/H{Dde�I fragmenrttogetherwithaverysmallfragmenrtthatrano thegel(see2.3.3.3).W~TVoasserttheconstraintthatthe0.47kbE/Hfragmenrtisthesameasthe0.45kbE/H|Dde�Iqfragment,Tclickon\Add"intheconstraintswindorw,andchoSose\Identical"fromthepopupmenruthatappears.Then,simplyclicrkonceG[oneacrhofthetwobands.NTheconstraintwillappSearinthe\Constraints"window.Norwclickon\Make,Maps"andyou'llgetjustonemap."ʫ1.1.72Sa=vingtoaFileYVoucansarveyourmapto le,CwhichcanbSeprinted.O!Justclickon\Save"inthe\Maps"windorw.AZpSopup[menuappSears.Choose\Save,CurrentMaptoFile".AnotherpSopupappSears:crhoose\Save,MapinaNewFile".iAzdialogbSorxappears;,trypeinthenameoftheԢ leyrouwanttosaveyourmapin, thenhitthe\return"key(and, fortheX11version,clicrkon\ACCEPT").YVourmapisondisk.2d�6�����������������������������������������F/B3��dCHAPTER1. #GETTINGSTVARTEDdd[cDDmanrualr�rGn؍1.2-CDataEnrtry7pDataIcanbSeenrteredintoDDIdbythreemethoSds:Rbyplacingbandsonthegelwiththemouse,UMbrytypinginfragmentsizes, zorreadinga lemadewithDDoratexteditor.TVouseanyofthesemethoSds,1eclicrkon\Digests".Thepopupmenruthatappearshastrwochoicesatthetopundert\Interactive,DataEntry": (wonethatreads\Method1:GraphicalInterface"andNanotherthatsarys\Method,2:TypeinValues".eYVouNhavealreadyloadeda le:thearvXailable3 lesinyourcurrentdirectoryorfolderarealsolistedonthemenu.Inthisexample,yrou'llseehowtousethemouse."ʫ1.2.12GraphicalDataEn=tryMWith,�thismethoSdofdataenrtryV,<Vyou,�placebandsintheDD+gelinthesameplacesrelativretov+standardsastheyareinyrourgel. jChoSose\Method,1:GraphicalInterface"v+fromthe\Digests"pSopupmenru.)6YVouwillneedasetofstandards.ChoSosethestandardsyrouusedHinyrourgelbyclickingon\Other"under\Digest,Data",ȰandchoSose\Choose,LaneStandard"fromthepSopupmenru.,ThenextpopupmenrugivesyouachoiceoftheavXailablestandards.vNoticethatthestandardscomeupwithadefaulterrorofzero.NorwyoucannameVyrourdatasetbyclickingonthetitle(\New-1")aftertheword\Digest:"thatappSears)]underthemenrubar.A)Ldialogborxwillappeartoenrterthenameofyourdataset.YVoutellDDwhicrhenzymesyouareusingbyclickingontheenzymenamesabSovethesingledigestlanes,�crhoSosing\Change,Enzyme"fromthepopupmenru,�andenteringanewenzymenameinthedialogbSorxthatappears.TVo{placeyrourfragmentsonthegel,pclickonthenameofyourenzyme,pandthenchoSose\Add,NewFragmentsviaMouse"&#fromthepSopupmenru.QNow&#asyrouplacethepoinrterinagellane,DDshorwstheequivXalentfragmentsizeinkbonthetopofthegellane.<MovethepSoinrtertotheapproximateplacewhereyourbandis,andpressdownthemousebutton.WhileDholdingthemousebuttondown�,gmakreA neadjustmentstothepSositionofthebandwhile>wratchingthefragmentsizereadout.1gWhenthebandisinthecorrectpSosition,غreleasethePmousebutton.RepSeatforallthebandsinthatlane.YVougetoutofdataenrtrymoSdebymorvingthepSointeroutofthe\Digest,Data"window.NoticethatDDdisplaysthetotalsize.ofallfragmenrtsinalaneatthebSottomofthatlane.>rAtanypSoint,Pyoucaneditthedata\thatyrouareentering.TVoedit,8getoutofdataentrymoSdeifyouareinit.ClickonthebandLyrouwanttoadjustorremove,5thechoSosetheappropriateoptionfromthepopup(see2.3.1.1LformorewraysLofediting).Whenyrouaredone,uyouwillprobablywanttosaveyournewdata:8select\Save"(see2.3.2fordetails)inthe\Digest,Data"windorw.1.2.22T=ypinginValuesMChoSose M\Method,2:TypeinValues".YVouwillneedtotellDD thenameofyrourdataset,®theznameofeacrhofthetwoenzymesyouused,®andthefragmentsizesineachofthethreeolanes.xYVoutrypSedataintoallsixareasinthesamewayV.xPointatadataentryarea.2d�7�����������������������������������������Z/B3��dCHAPTER1. #GETTINGSTVARTEDdd[cDDmanrualr�rGnAhbSorxappears.GClickthemouse.GYVouarereadytoenterdata.GAsyoutypSe,0thelettersUMand~nrumbSersappearinatypewriter-stylefonrtwhichtellsyouwhichinputareaisactive.Whenyrouaredone,press\return".6ThetypSewillgobacktotheusualDDofont.6WhenenrteringQfragmentsizes,M;youcanusebporkb;%bSesuretoseparatethefragmentsizesbyspaces.gNYVou"cancrhangethedataenteredinagiven eldbyclickingonitagain.gNWhenyouare<doneenrteringdata,QYclickon\ACCEPT".YVoucansavethisdatasettoa lebychoSosing\Save"inthe\Digest,Data"windorw.(V1.3-CDoingMoreWithDD7pDD}givresЄyoumanywaystoexpressfactsabSoutyourdata.0)YVoucanseterrorrangesbygel,brySlane,nNandbyfragment.tTheseerrorscanbSespeci edbrysizeerrororbyerrorbasedonmigrationdistance.gYVoucantellDDthatafragmenrtinonelaneisidenticalto,Ӊisbiggerthan,isE;smallerthan,conrtains,ordoSesn'tconrtainafragmentinanotherlane. HYVoucandisplaryhmapsstartingfromanydoubledigestfragment. DDhallowsyoutomanageyourdataandmapsbrykeepingtheminwhatever lesyoulike.#MMoreover,youcanstoreyourmapsastextorpSostscriptgraphics.YVou'probablynoticedmanryofthesepSossibilitiesasyouwentthroughthe rstexample.Theyarediscussedinthereferencesectionofthismanrual.2d�8��� ��������������������������������������/B3nHChapter 22��Reference6UMInthiscrhapteryouwill ndalistofallofthecapabilitiesofDDandhowtousethem.&YVouUMprobably3wron'twanttoreadthissectionallthewaythrough.-dYVoumaywanttoloSokthingsupinitfromtimetotime,andsothe rstsectionofthiscrhapterexplainshowthereferencesectionoDisorganizedandhorwtouseit.ThismanualisalsoavXailableasonlinehelp.TVomakeDD6morewconrvenienttouse,%kthereisusuallymorethanonewaytodosomething.,MEverycommand*hasaheadinginthiscrhapteralthoughwehaveusedcrossreferencestocutdownonredundancyV.(V2.1-CSixMainWindorws7pDD5has<foursubrwindows<ofitsmainwindorwandoptionalonesforhelpandshowingmatchdetails.FVorH1eacrhofthefoursubwindowsandtheoptional\Match,Details"windowthereisa^sectionlikrethisone.5rIfyougiveDD[acommand,myouaredoingitfromacertainwindow,and thatisthesectionofthemanrualthatyouloSokinto ndthecommand.ThesubheadingsinthismanrualhavethesamenamesasthecommandstheydescribSe.TheWbSeginningofasectionaboutaparticularwindorwbrie ydescribestheinformationdisplaryed WinthatwindorwaswellasthethingsthatDD doSesthatyoucontrolfromthatwindorw."ʫ2.1.12ButtonsMYVougivrecommandstoDDbyclickingwiththemouseandchoSosingfrommenus.mInthismanrual,aplaceyoucanclickontogiveacommandiscalledabutton.+Mostbuttonsarewrords,YlikeW5\Make,Maps",andmostoftheseareloScatedinarorwacrossthetopofeachsubrwindow.eWVerefertothisrorwofbuttonsasthemenubarforthatsubwindow(nottobSeconfusedwiththeMacinrtoshmenubar).Somebuttons, �likethebandsonthegelinthe\Digest,Data"windorw,arenotwords.Evrerybuttonthatisvisibleonthemainwindowhasitsownsubsection.AThebSeginningofasubsectiondescribSeswhatthebuttondoes,ϗifitdoessomethingbryitself.-Mostbuttons2�9��� ��������������������������������������H/B3��dCHAPTER2. #REFERENCEdd[cDDmanrualr�rGnexpSectyroutomakefurtherchoicesfromamenu.MIfso,3ItherewillbSefurthersubsectionsUMabSouteacrhmenuchoice.2.1.1.13�P�opup�Menus.MDDHhasqmanrypffopupQmenus.:TheyaremenusofafewitemsthatappSearafterclickingonabuttonoranitemofanothermenru.$Theygoawayafteryouclickonamenuchoiceor,inGkX11,^ifyrouclickoutsidethemenu.O(Eachalsohasa\CANCEL"GSbutton.O(UsuallyyougiveDDAaWcommandbryclickingonabuttonandchoSosingfromapopup,butsometimesyrouwillneedtocrhoSosefurther,eitherthroughanotherpopupmenruoradialogborx.Dialog~Bo�xes. Dialog bSorxesexpectyroutotypSesomethinginorreadamessage,7bandwon'tletpyrouproSceedfurtheruntilyoudo.#IfyouchangeyourmindabSoutusingadialogborx,Hjustclicrk\CANCEL".YVoumayhavetohit\return" rst.*YVoucangetoutofadialogbSoxwithamessage4%bryclickingon\OK".UnderX11,FyoumayhavetoclickonadialogbSoxtotypSeinit,depSendingonhorwyourwindowmanagerissetup.Ho�wFDoIFbGiveThisCommand? OccasionallythecommandyrouwantwillbSeratherdeeply_buriedinacrhainofsubmenus.Thischapterisorganizedtohelpyou nditeasilyV.FVor@example,fsuppSosethatthisparagraphdescribedwhatyrouwantedtodo.2Thatmeansthe{ybSoldheadingofthisparagraphisthenameofthecommandasitappearsonamenru.YVou'dgivrethecommandbygoingtothewindowdescribSedin2.1,clickingonthebuttondescribSedҴin2.1.1, crhoosing2.1.1.1, crhoosingthemenruitem\Dialog,Boxes", and nallycrhoSosing>thecommanddescribedhere,awhicrhwouldappSearonthemenuas\How,doIgivethis,command?".(V2.2-CTheTXopWindorw7pThis7isthegeneralinformationwindorwofDD.UsuallyV,JitdescribSesimportanrtinformationabSout)NwhatevrercomponenrtofDD)>themouseispoinrtingto.FVorexample,8whenthemouseispSoinrtingtoabandonthegel,RitgivesinformationabSoutthesizerangeofthatfragment.WhenjDDiscalculatingmaps,itshorwsthestatusofthecalculation. %Whende ningaconstrainrt,ythe]topwindowinformsyouthatDD]iswaitingforyoutoselectafragment. Thetopswindorwisalsousedforthedisplayofmatchinformationselectedintheoptional\MatchDetails"windorw(see2.6). ,Themenubarofthiswindowhasthreebuttons,^called\Help",\Configure",and\Exit"."ʫ2.2.12HelpMGetsyrouthismanualonline.WhenyouchoSose\Help",papopupmenruappearswiththemainheadingsofthismanruallisted.ClickonaheadingtomakethecorrespSondingsectionof5themanrualcomeupinahelpwindow.4TVoscrollupordowninthehelpwindow,usethe2d��10��� ��������������������������������������Ƞ/B3��dCHAPTER2. #REFERENCEdd[cDDmanrualr�rGnscrollZ`barontheside.Theenrtirescrollbarrepresentsthewholemanual,vNandthestippledUMpart)~represenrtsthepartthatisinthewindow.cWhenyouclickwiththemouse,94thetopoftheTstippledareaofthescrollbarwillmorveTtothepSoinrter,andthecorrespondingpartofthemanrualwillbSecomevisible.YVoucangetridofthehelpwindorwbyusingtheclosebSox(Mac)oryourwindowmanager(X11).ߖUnlikrewamenu,thehelpwindowdoSesnotgoawayunlessyouexplicitlydismissit.YVouVcanuseDD%withthehelpwindorwup.nIfyouneedto ndsomethingfromthemenuofu/topicsafterusing\Help",justcrhoSose\Help"again,andselectfromthemenru. uTheappropriatesectionofthemanrualwillappSearinthe\Help"window."ʫ2.2.22Con gureMUsethisbuttontosetthedefaultdatadirectoryV,Rcolor,andwhetherdetailsofmapbuildingareshorwn.2.2.2.13�Displa�y�inMono`�chrome/Color.TVoggle9bSetrweencolorandmonoSchromeversionsofDD.DD9iseasiertoseeinmonoSchromeonmonoScrhromemonitorsandcertaingrayscaleorcolormonitors.2.2.2.23�Set�DefaultDataDirectory�.The_udefaultdatadirectory(or\folder")isthedirectorythatDD_RstartsfromtoloSokforandcreatedata lesandmaps.73Thisoptionallorwsyouto ndoutwhichfolderDDisnowusingasadefault,andcrhangeitifnecessaryV.AcceptR(Directory<curren�tdirectory>. ChoSosingthisoptiontellsDD·thatyrouwantto<usethecurrenrtdirectory(folder)asthedefault.ĝUsethistokeepyourcurrentdirectoryorvcrhoSoseanewoneaftermovingthroughthedirectorytreewiththe\Subdirectories,ofCurrent,Directory"or\MoveUpDirectoryTree"options.Sub`�directories ofCurren�tDirectory�. Alist9ofsubSdirectories(folders)ofthethecurrenrtdefaultdirectory(folder).eChoSosingoneofthesewillcauseanewmenrutoappearwiththecrhosensubSdirectoryasthenewcurrentdirectoryV.Mo�veڍUpDirectoryT�ree. MorveZtotheparenrtdirectory(folder)ofthecurrentdirectory(folder). lChoSosingQ<thisoptionwillcauseanewmenrutoappearwiththeformerparenrtdirectory(folder)asthenewcurrenrtdirectory(folder).Macin�toshDialogBox. SetkdthedefaultdirectorywithastandardMacinrtoshdialogbSox.2d��11��� ��������������������������������������M/B3��dCHAPTER2. #REFERENCEdd[cDDmanrualr�rGn2.2.2.33�Sho�w�DetailsofMapBuilding.MChoSosing1thisoptioncausesthe\Match,Details"windorwtobedisplaryed.zThis1windowUMshorwsdetailsoftheintermediatestagesofDD'scalculations(see2.6).5GTVostopshowingthedetails ofmapbuilding,Tclicrkonthe\Close,Window"button,theclosebSorx(Macintosh)oruseyrourwindowmanagertoquitthewindow(X11)."ʫ2.2.32ExitQuithiDD.OnaMacinrtosh,vyouhicanalsoquitbryclickingontheclosebSoxorchoSosing\quit"fromtheMacinrtosh\file"menu.IfyouareusingDDunderX11,youcanalsoquitusingyrourEMwindowmanager. HIfyouhavedataormapsthathavenotyetbSeensavedtodisk,DDwillputupadialogbSorxthatwarnsyouabSoutthisandasksifyoureallywanttoexit.Clicrknon\Stop,toSaveData"ntoabSortthe\Exit"command,3 orclickon\Exit,DD"+toexitanrywayV.(V2.3-CTheDigestDataWindorwӡThe{\Digest,Data"windorwisdividedintothreesections,ofwhichthebSottomone(settings)can )bSesuppressed,8learvingonlytwosections.Thetopsectionisthemenubar.IthasbuttonslabSeledlq\Digests",\Save",\Error",and\Other".:Themiddlepartisthegelsection.ItshorwsHagelwiththreelanes;anoptionalstandardslanemaybSeshown. RAH?sizescaleisprorvidedoontheright.Y6Thenameofthedatasetisshownatthetopfollowingtheword\Digest:".Itisabutton.EacrhlaneislabSeledatthetop,andthelabelsarealsobuttons.OnIeacrhlaneofthegelfragmentsaredisplayedwitherrorbars,qandeachfragmentisanactivrebutton.Thefragmentsinthetwoenzymelanehavetwosetsoferrorbars.WhenDDis`]toldthedataisfromthesamegel,|bSothsetsareshorwn. Theinneronesareusedfor\samegel"dataandtheouteronesfordatafromdi erenrtgels.WhenDDistoldthedataisfromdi erenrtSgels,nEonlytheerrorbarsappropriateforthatsituationareshown.tAtthebSottomofqeacrhlanethetotalsizeoffragmentsinthatlaneisshown,togetherwiththeminimumand,maximrumlimitsofthattotalconsistentwiththeerror.#aThesettingssection,ifpresent,shorws thedefaulterrorlimits,'ewhetherornotDDistreatingthedataasbSeingfromthesame gel,bthemaximrumsizeofunseenfragmentsforDDtousein ts,bandthemaximumnrumbSerofsucrhfragmentsthatDDcanusepSermatchedgroupoffragments."ʫ2.3.12DigestsThisbuttonpSopsupamenruthatisusedforenteringanewdatasetorchoSosingoneondisk.8DataSetsondiskcanbSecrhosenfromthedefaultdirectoryoranyother.2d��12��� ��������������������������������������ʠ/B3��dCHAPTER2. #REFERENCEdd[cDDmanrualr�rGn2.3.1.13�Metho`�d�1:��GraphicalIn�terface.MChoSosethisinordertoenrternewdigestdatawiththemouse.wDDwillremindyoutosaveUMyrourdatatoa lebSeforeyouquit.NamezofLane. Clicrk:onthenameofthegellanetoaddnewfragmentstothatlane(bymouseorkreybSoard),tochangethenameofthelane,ortochangethedefaulterrorestimateforthatlane.AddNewF�ragmen�tsviaMouse. ChoSoselBthistoaddoneormorefragmenrtstothatlaneRwiththemouse.OnceyrouchoSosethisoption,DDHwillbeindataenrtrymodeforthatlaneunrtilthepSointerleavestheDigestDatawindow.fYVoucanenterasmanybandsasyouwrantwrwithoutlearvingdataentrymoSde.yIndataentrymoSde,}DDwUshowsthemolecularweightcorrespSondingtothecurrenrtpoinrterpositionatthetopofthelanethatdataisbeingenrteredin.(Depressingthemousebuttonplacesathinbandwithnoerrorbarsonthelane,kbut nescale\adjustmenrtstotheloScationofthebandaremadewhilethebuttonremainsdepressed.When'thebuttonisreleased,Gthebandisplacedonthegel.v^ThelinerepresenrtingthebandbSecomesthicrkerandnowhaserrorbars.AddNewF�ragmen�tsviaKeyb`�oard. ChoSosingEthisoptionbringsupadialogborxthat allorwsyoutotypSeinthesizeofanewfragment.TypSeinthenewvXalue,6press\Return",andclicrkon\ACCEPT"toenterthenewfragment.BetweenthetimeyouclickonthevXalue eld@?andthetimeyroupress\return",Uthe\CANCEL"@)buttonwon'twork.9Ifyou'vestartedtryping׷andchangeyourmind,ہpress\return"andthenclickon\CANCEL".Ifyouwantthisfragmenrt'syerrorrangetobSedi erentfromthedefault,clickon\Set,ErrorRange".YVoucanthenselectanewerrorrangefromthepSopupmenru.ChangeEnzyme. ChoSoseqQthistoenrteranewenzymenameatthetopofagellaneorcrhangetheonethatisalreadythere.EDDwillincludealltheenzymesthathavebSeenenrteredaspSossiblechoices.)Iftheoneyouwantisnotthere,ƐchoSose\Enter,EnzymeName".A@dialogA bSorxwillcomeupforyoutoenterthenameofyourenzyme.�WEnterthenameofyourenzyme,press\return",andclicrkon\ACCEPT".Untilyoupress\return",the\CANCEL"button?wron'twork.Ifyou'vestartedtypingandchangeyourmind,bpress\return"andthenclicrkon\CANCEL".ChangeSize-EstimateErrorRanges. ThisNgivresyouamenuthatyoucanusetoinputtheerrorrangeforthegellaneyrouhavechosen.8FVordetails,see2.3.3.1.2.3.1.23�Metho`�d�2:��T�ypeinV�alues.MUse�thistotrypSefragmentsizesdirectlyfromthekeybSoard.{YVouwillgeta\Define,NewData,Set"dialogbSorx,=whichwillaskyrouforthenameofyourdataset,=thenameofeachof2d��13�����������������������������������������[/B3��dCHAPTER2. #REFERENCEdd[cDDmanrualr�rGnthe1trwoenzymesyouused,andtheerrorrangefortheentiregel(\Global,ErrorRange").De neLNewDataSetDialogBo�x. There aresixareasforenrteringdatainthisdialogUMbSorx.Oneistotherightof\Name:",X,thatisforthenameofyourdataset.Twoothersarevtotherighrtof\Enzyme,1:"Qwand\Enzyme2:"Qw. Thoseareforthenamesoftheseenzymes.�Threexdataenrtryareasaretotherightof\Sizes:".�Theseareforenteringtheactual fragmenrtsizes.L Abutton,2\Set,GlobalErrorRange",allorws yousetthedefaulterrorrangeforthewholegel.5YVoutrypSedataintoallsixinputareasinthesamewayV.5Pointatadataenrtryarea.|AbSoxappSears.|Clickthemouse.|YVouarereadytoenterdata.|AsyrouőtypSe,thelettersandnumbSersappearinatypewriter-likefonrtwhichtellsyouwhichinputareaisactivre.x9Whenyouaredone,E press\return".x9ThetypSewillgobacktotheusualcDDRfonrt."Whenenteringfragmentsizes, youcanusebporkb;%bSesuretoseparatethefragmenrt}Msizesbyspaces.FVorcertainsizesthatmakesenseasbporkb,DD}'mayaskyouwhicrhoftheseyoumeant.JYVoucanchangethedataenteredinagiven eldbyclickingonitagain.8Whenyrouaredoneenteringdata,clickon\ACCEPT".GlobalErrorRange. This"ngivresyouamenuthatyoucanusetoinputtheerrorrangefortheenrtiregel.8FVorfurtherdetails,see2.3.3.1.2.3.1.33�Loaded�FilesandDoubleDigests.MThis#menruchoiceallowsyoupickadigestfroma lethathasalreadybSeenloadedbyDD,or^toreloada leafteritortheactivredatasethavechanged.oEachloaded leisshown,follorwedbyanindentedlistofofeachdatasetinthat le.IfyouchoSosethe lename,,DDwill pSopupamenruandaskwhichofthedatasetsinthat leyouwant.AlternativelyyoucansimplycrhoSosethedesireddatasetfromtheindentedlist.2.3.1.43�Other�FilesinDataDirectory�.MThisheadingonthemenruisfollowedbyalistofallofthe lesinthecurrentdirectoryV.Clicrkoona lenametoloadthat le.IfDDncannotinterpretthe leyouhaveselected,,itwillprinrtanerrormessage.2.3.1.53�Sub`�directories�ofDataDirectory�.MThisj@headingonthemenruisfollowedbyalistofsubSdirectories(folders)ofthepresentdirectoryV.IfԔthedata leyrouwantisinacertainsubSdirectoryV,clickonitsname.AXnewmenru;JwillappSearofthe lesinthatsubdirectory(folder).*Loadthe leyrouwantormovetoanewdirectoryV.2d��14�����������������������������������������+/B3��dCHAPTER2. #REFERENCEdd[cDDmanrualr�rGn2.3.1.63�Mo�ve�UpDirectoryT�ree.MIf3 thedata leyrouwantisintheparentdirectory(folder)ofthecurrentdirectoryV,E"clickonUMthis[crhoice.A[{newmenuwillappSearofthe lesintheparentdirectoryV.Loadthe leyouwrantormorvetoanewdirectoryV."ʫ2.3.22Sa=veUseQ�thisbuttontosarveQ�yourdatatoa le.TVogetherwithyourdata,oDDPwillsaveallcurrentconstrainrtsanderrorranges.-YVoucansaveyourdatatoany le,ϗwhetherneworpreviouslyexisting.(Ifzthe leyrouaresavingtoexists,youcanappSendyourdatatotheendofitororverwriteithe le. This\Save"buttonisonlyforsarvingdata.TVosarveimaps,usethe\Save"buttoninthemenrubarofthe\Maps"window.2.3.2.13�Sa�ve�DatainaNewFile.ChoSosethistosarvedatatoanew le."AdialogborxwillappearsothatyroucantellDDthenameofthe letosarveto.Sa�ve}DataInNewFileDialogBo�x. Enrterthenameofthe leyouwanttosaveyourdatato,gpress\return",andclicrkon\ACCEPT".The\CANCEL"buttonwon'tworkuntilyoupressF\return",soifyrou'veFstartedtrypingandchangeyourmind,press\return"andthenclicrk on\CANCEL".Ifyouenterthenameofa lethatalreadyexists,IDD jwillcomplainabSoutyrourchoiceandleavethat leintact.2.3.2.23�App`�end�DatatoanExistingFile.MChoSosexthistosarvexdatabryappendingittotheendofanexisting le.UnderX11,yrouhavethe+ rsttrwo+menuchoiceslistedbSelow,whileontheMacintoshyougettheMac ledialogbSorx.Con�tents ofCurren�tDataDirectory<directoryname>. ThisDheaderappSearsabSorvealistofall lesandsubdirectoriesinthecurrenrtdirectoryV.2HFilesarelistedsimplybyname;subSdirectoriesarelistedasacompletepathwithleadingandtrailingslashes.ChoSosinga lenamewillcauseDDztoappendyrourdatatotheendofthat le.Caution:DDwillnotcrheckifthe leyrouareappSendingtocontainsvXalidDDdata.nIfitdoSesnot,DDwill appSendthedataanryway butmarynotbeabletoreadit.+WInthatcaseyrouwillhavetoeditthesarved lebryhand.ClicrkinghonthenameofasubSdirectorywillcauseanewmenutoappSearthatcontainsthe lesandsubSdirectoriesinthecrhosensubdirectoryV.0FSarvetothe leyrouwantormovetoanewdirectoryV.2d��15�����������������������������������������Ϡ/B3��dCHAPTER2. #REFERENCEdd[cDDmanrualr�rGnMo�veupDirectorytree. MorvesCeyoutotheparentdirectoryV.CACNnewmenuwillappSearUMof"Ythe lesandsubSdirectoriesoftheparenrtdirectoryV.Savetothe leyouwantormovetoanewdirectoryV.Macin�tosh;FileDialogBox. OnxtheMacinrtosh,(youxwillgettheusualMacdialogbSorxforcrhoSosing les.8UseitasyouwouldinanyotherMacintoshapplication.2.3.2.33�Replace�DatainanExistingFile.MChoSose^thistosarve^datainanexisting lebryreplacingthedatathatisalreadythere.Caution:8DDwillerasetheolddatainyrour leifyouchoSosethis.FVoroptions,seeprecedingsection2.3.2.2."ʫ2.3.32ErrorThisbuttonallorwsyoutocontrolhowDDdealswithexpSerimentalerrorovertheentiregel.YVoucanusethisbuttontosetdefaultuncertainrtyforeacrhbandonthegel.XYoucanuseitto:tellDD:thatyrourdatacamefromthesameordi erentgels,NsothatDD:dealswiththeerrorRaccordinglyV./YoualsousethisbuttontotellDDRmthesizeofthelargestunseenfragmenrtthatDDcanusetomakreamap,andhowmanysuchunseenfragmentsitisallowedtousepSermap.2.3.3.13�Change�Size-EstimateErrorRanges.ChoSosingthisgivresyouamenuthatyoucanusetoinputtheerrorrangefortheentiregel.NoteUthatthecurrenrtrangeforthewholegelisgiven.=YVoucangivedi erenterrorrangesforparticularlanesbryclickingonthenameofthelaneandforparticularfragmentsonthegelbryclickingonthem.YVoucanspSecifyerroreitherasfragmentsizeerrorin%,orasstandarddeviation..LoSosely̻speaking,ҷstandarddeviationisanerrorestimatebasedonmeasuremenrtuncertainrtyooftheloScationofabandonthegel.Thisestimateiscomrbinedwithanestimateof&likrelysystematicerrorsforsmallfragmentstogetanoverallcon dencelevelforerrors.2.0standarddeviationsisourbSestguessfor95%con dencelimitsonatrypicalgel.2.3.3.23�Change�BasisofSizeComparisons.Usethismenruchoicetocontrolhowerroristreatedinthetwo-enzymedigestlane.!(ThecurrenrtKsettingisshowninparentheses. Z:TherearetwopSossiblesettings,8\Same,Gel"or\Separate,Gels".oSmallererrorrangesareusedinthetrwo-enzymelaneifthedatawrerefromthesamegel.IfDD~issetto\Same,Gel",%bSothsetsoferrorbarsareshorwn.Thesmaller\Same,Gel"yerrorbarsareclosesttothecenrter.2{ThismenuchoicegetsyouasubmenuthatlistsbSothcrhoices.2d��16�����������������������������������������/B3��dCHAPTER2. #REFERENCEdd[cDDmanrualr�rGnSame6Gel. TVreatv6errorsforthedoublydigestedfragmenrtsasifallthedatacamefromtheUMsamegel.SeparateGels. TVreatDHerrorsforthedoublydigestedfragmenrtsasifthedatacamefromseparategels.2.3.3.33�Unseen�F�ragmen�ts:��SizeCeiling.MUsecthismenruchoicetotellDDbthesizeofthelargestundetectedfragmentonyourgel. YVoumighrtͿnothavedetectedfragmentssmallerthanthisbSecausetheyrano theendofthegelor[GstainedtoSowreaklyV. Thecurrentsizeceilingisshowninparentheses. ChoSosingthiscausesanewpSopupmenrutoappearthatgivresyouachoiceofpSossiblesizeceilings.SizeCeilingMen�u(0bpto4000bp). Picrkf[yourchoiceforanewunseenfragmentsizeceilingfromthismenru.2.3.3.43�Unseen�F�ragmen�ts:��Numb`�erAllowedPerMatch.MUsethismenruchoicetocontrolhowmanyundetectedfragmentsDDcanuseinmatchingeacrhsingledigestfragmentwithfragmentsfromthedoubledigestlane(see2.6).ChoSosingthis0~causesanewpSopupmenrutoappearthatliststhearvXailablechoices.ThecurrentnumbSerisgivreninparentheses.Num�b`�er͵ofUnseenF�ragmentsmenu:(0,^1,2). UseOzthismenrutopickyourchoicefortheumaximrumnumbSerofunusedfragmentstobSeusedineachgroupofmatchedfragments."ʫ2.3.42OtherMUsekthe\Other"buttontotellDDAhorwtodisplayDNAAsizestandards,toaskDDabSoutpSossibleinconsistenciesinyrourdata,tocontrolwhetherthebSottomsectionofthe\DigestData"VVwindorwisdisplayed,t�torenameyourdigest,t�and(ifyouknow)totellDDV1ifyourDNAislinearorcircular.2.3.4.13�Cho`�ose�LaneStandard.MUsegthismenruchoicetochoSoseasetofsizestandardstodisplayV. YougwillgetapSopupmenuthatgivresthecurrentlyavXailablestandardsasachoice,aswellas\None",whichremovesthe: standardslane.' ThecurrenrtlyavXailablestandardsincludelambSdaHin�DIII9andBst$DEIIfragmenrts+5aswellasthe1kbladder,{X123kbladder,andhighmolecularwreight+5markersfromBRL.Ifthestandardsyrouusearenotonthemenu,byoucanaddthem.*LoSokfora lecalled 8\standards"inthedatafolderthatcamewithDD.Addyrourstandardinthesameformatusedfortheothers..pBesurethe rstlineofyrourstandardsdatareads\dataset:restriction-gel-standard",_ putthenameofyroursetofstandardsafter\name:",and2d��17���������������������������������������� 1/B3��dCHAPTER2. #REFERENCEdd[cDDmanrualr�rGnplaceMthefragmenrtsizesinacolumnstartingonthelinefollowing\fragments:".WhenUMyrou5are nished,Hsavethe leasASCISI5text.BecarefulnottosaveitasaformattedwordproScessor( le. _YVoucanputyroude nitionsinaseparate le,+andloadthemusingthe\Digests"l leselectionmenru, oryoucanappSendthemtothe lenamed\standards"whichisloadedautomaticallywhenDDstartsup.2.3.4.23�Drop�LaneStandard.MChoSoseTthistostopdisplaryingthestandardslane,?anddropitsassociationwiththedataset.Theotherthreegellaneswillwidento lltheextraspace.ItisanarvXailablechoiceonlyifstandardsarecurrenrtlybSeingdisplayed.2.3.4.33�Hide/Sho�w�LaneStandard.MThisUmenruchoiceturnsdisplayofthestandardslaneonoro ,sbutmaintainstheassoSciationof|astandardwiththedataset.k\Itisonlydisplaryed|whenastandardhasbSeencrhosen,andreads$\Hide"or\Show"depSendingonwhetherstandardsarecurrenrtlyshownorhidden.Theotherthreegellaneswillwidento lltheextraspace, ornarrorwtomakeroSomforthestandardslane.2.3.4.43�Critique�Curren�tData.MChoSose6thistocrheck6yourdataforconsistencyV.DD6willcheckthatalllanesadduptothesamemolecularwreight(withinerrorlimits).cDDowillalsocounrtfragmentsinthedoubledigestlanecomparedtothesingledigestlanesandtellyrouifthefragmentnumbSerslookstrange~orsuggestlinearorcircularDNA.Afteryrouhavereadthecritique, clickon\OK".Itis$>agoSod$>ideatousethiscapabilitryofDD$/afterenteringanewdataset.DataiscritiquedautomaticallyӇafterbSeingloadedfroma le. |Also,MdatathatyrouhaveenteredwillbSecritiquediautomaticallywhenyrouclickon\Make,Maps"ifithasnotbSeencritiquedbeforeorifithasbSeeneditedsincebeingcritiqued.2.3.4.53�Hide/Sho�w�Settings.MUseythismenruchoicetohideorshowthesettingssectionatthebSottomofthe\DigestData"windorw.Thegellaneswillexpandandusetheextraspace.Hidingthissectionisoftenusefulwhenenrteringdatagraphicallyonasmallmonitor.2.3.4.63�Rename�Digest.MUse|.thismenruchoicetorenameyourdataset.sAn\Enter,NewDigestName"|.dialogbSoxwillappSear.GTrypeinthenameofyrourdigestandclickon\ACCEPT".BetweenthetimeyoubringupthedialogbSorxandthetimeyoupress\return",the\CANCEL"buttonwon'twork.Ifyrou'vestartedtypingandchangeyourmind,press\return"andthenclickon\CANCEL".2d��18����������������������������������������;/B3��dCHAPTER2. #REFERENCEdd[cDDmanrualr�rGn2.3.4.73�Set�DNAT�yp`�e.MUserthismenruchoicetotellDD*ifyouknowwhetheryourDNA*islinearorcircular.#ChoSosingUMthiswillcauseapSopupmenrutoappearwiththecrhoices\Circular",v\Linear",orboth.ChoSosingf\Linear"willconstrainDD[to ndmapswithatleastonecoincidence(commoncuttingsiteforbSothenzymes)."ʫ2.3.52Digest:\%5 b>�ff� ���cmmi10<Title>Clicrkonthisbuttontorenameyourdigest.xAn\Enter,NewDigestName"dialogbSoxwillappSear. Trypebinthenameofyourdigestandclickon\ACCEPT".BetweenthetimeyoubringupthedialogbSorxandthetimeyoupress\return",the\CANCEL"ybuttonwon'twork.{Ifyrou'vestartedtrypingandchangeyourmind,press\return"andthenclickon\CANCEL"."ʫ2.3.62GelLaneTitleClicrkAonthegellanetitletoaddnewfragmentstothelanebymouseorkeybSoard,Vandtocrhangeberrorrangeforthatlane.Ifyouclickonthetitleofasingleenzymelane,youcanalsocrhangethenameoftheenzymeinthatlane.%ClickingonthetitleofthestandardslaneenablesyroutochoSoseadi erentsetofstandards.2.3.6.13�Add�NewF�ragmen�tsviaMouse.ChoSoseZthistoaddoneormorefragmenrtstothatlanewiththemouse.#OnceyouchoSosethisoption,DDwillbSeindataenrtrymodeforthatlaneunrtilthepoinrterleavestheDigestDatawindorw.;YVoucanenterasmanybandsasyouwantwithoutleavingdataentrymoSde.IndataenrtrymoSde,DDshowsthemolecularweightcorrespSondingtothecurrentpSointerpSosition8atthetopofthelanethatdataisbeingenrteredin."kDepressingthemousebuttonplacesQathinbandwithnoerrorbarsonthelane,but nescaleadjustmenrtstotheloScationofZthebandaremadewhilethebuttonremainsdepressed.!Whenthebuttonisreleased,6thebandisplaceedonthegel.ThelinerepresenrtingthebandbSecomesthickerandnowhaserrorbars.2.3.6.23�Add�NewF�ragmen�tsviaKeyb`�oard.ChoSosing؟thisoptionbringsupadialogborxthatallowsyoutotypSeinthesizeofanewfragmenrt.hClick@onthenrumbSer@torighrtof\Size:".TrypSeinthenewvXalue,press\Return",andclicrkon\ACCEPT"toenterthenewfragment.BetweenthetimeyouclickonthevXalue eld@?andthetimeyroupress\return",Uthe\CANCEL"@)buttonwon'twork.9Ifyou'vestartedtrypingEandchangeyourmind,\press\return"andthenclickon\CANCEL".Ifyouwantitserror rangetobSedi erenrtfromthedefault,.clickon\Set,ErrorRange".ڣYVou willgettheerrorrangepSopupmenrutochoSoseanerrorrangefrom.2d��19����������������������������������������"/B3��dCHAPTER2. #REFERENCEdd[cDDmanrualr�rGn2.3.6.33�Change�Size-EstimateErrorRanges.MThisRgivresyouamenuthatyoucanusetoinputtheerrorrangeforthegellaneyouhaveUMcrhosen.zYVoucangivedi erenterrorrangesforparticularfragmentsonthegelbyclickingonthem.8FVorfurtherdetails,see2.3.3.1.#2.3.6.43�Change�Enzyme(orLaneStandard).ChoSose#thistoenrteranewenzymenameatthetopofagellaneorchangetheonethatisalreadyYxthere.OIfyrouclickedonthestandardslane,u+thechoicewillbSeamongtheavXailablestandards.DDuwillincludealltheenzymesthatharvebSeenenrteredaspossiblecrhoices.Iftheoneyrouwantisnotthere,choSose\Enter,EnzymeName"./Adialogborxwillcomeupfor yroutoenterthenameofyourenzyme.-ClickonthedialogbSox,Henterthenameofyourenzyme,[presse\return",andclicrkon\ACCEPT".BetweenthetimeyouclickonthedialogbSorxnandthetimeyoupress\return",~the\CANCEL"nebuttonwon'twork.|Ifyou'vestartedtrypingandchangeyourmind,press\return"andthenclickon\CANCEL".!Ͷ2.3.72BandonGelEacrhbandonthegelisalsoanactiveDDbuttonthatgivesapSopupmenuwhenclicked.Clicrk onagelbandto ndoutfactsabSoutthatbandortoassertconstraintsabSouttheband.&YVou alsocanclicrkonabandtosetitsindividualerrorrange,tochangeitssize,ortoremorveit.#2.3.7.13�Ab`�out�F�ragmen�t<enzyme,size>.DisplarysadialogbSoxthatcontainsbasicfactsabSoutthefragment,;includingitssizeanderrorrange.8Clicrkon\OK"tomakethisbSoxdisappSear.#2.3.7.23�Assert�Constrain�t.ThisvistheheaderforanindenrtedlistofconstraintsthatyoucanassertabSoutyourdata.Eacrh8constraintdescribSesarelationshipbetrweentwofragments,oneofwhichmustbSeasingledigestfragmenrtandtheotheradoubledigestfragment.AllpSossibleconstraintchoicesareasserted8=inthesamewrayV.!ChoSose8=theconstrainrtbyclickingononeofthebands.!Picktheconstrainrt'fromthemenu.Clickontheotherband.ThenewconstraintwillappSearintheconstrainrtswindow.#2.3.7.33�Iden�tical.ChoSosethistoassertthatyrourfragmentisidenticalwithanotherfragment.2.3.7.43�Not�Iden�tical.ChoSosethistoassertthattrwofragmentsarenotidentical.2d��20����������������������������������������//B3��dCHAPTER2. #REFERENCEdd[cDDmanrualr�rGn2.3.7.53�Bigger�Than.MChoSosethistoassertthatthefragmenrtyouclickedonisbiggerthananotherfragment.2.3.7.63�Smaller�Than.ChoSosethistoassertthatthefragmenrtyouclickedonissmallerthananotherfragment.2.3.7.73�Con�tains�(PartOf:).ChoSoseދthistoassertthatthesingledigestfragmenrtyouclickedoncontainsaparticularUMdouble-digestfragmenrt.wIfyouclickedonabandinthedoubledigestlane,>thismenuitemreads\Part,of".2.3.7.83�Not�Con�tains(NotPartof:).MChoSose>thistoassertthatthesingledigestfragmenrtyouclickedondoSesnotcontainaparticulardoubledigest.B-Ifyrouclickedonabandinthedoubledigestlane,thismenuitemreads\Not,Partof".2.3.7.93�Change�Size-EstimateErrorRanges.MChoSosethisifyrouwantaparticularbandtohaveanerrorrangedi erentfromtherangeselectedWforthewholedatasetorforaparticularlane.Thismenruchoiceallowsyoutoselecterror]rangefromamenru;Tforeven nercontrolsee\Change,SizeData".8The]errormenuisdescribSedin2.3.3.1.2.3.7.10:�Change�SizeData.MChoSosingthisoptionbringsupadialogborxthatallowsyoutotypSeinanewsizeforthefragmenrtDyouclickedon.GYVoucanalsosettheerrorrangetoanyvXaluesyoulike.GTVoentera>newfragmenrtsize,RclickonthenumbSertorightof\Size:".3TypSeinthenewvXalue,Randpress\Return".+TVosettheerrorrangetoyrourexactspSeci cations,entertheminimumandmaximrum/pSossiblesizesforthefragmentafter\Min:"7#and\Max:"respSectivrelyV,justasyoudidZforthesize eld.Ifyrouwanttosettheerrorfromtheusualmenu,wclickon\Reset,SizeRange"U>andcrhoSosetheerrorrangeyouwantfromthemenu.xIfyoudothis,otheminimumand$maximrumvXalueswillbSeadjustedautomaticallyV.BetweenthetimeyouclickonthevXaluef eldandthetimeyroupress\return",Uthe\CANCEL")buttonwon'twork.Ifyou'vestartedtrypingandchangeyourmind,press\return"andthenclickon\CANCEL".2.3.7.11:�Remo�ve�F�ragment.MChoSosethistoremorveafragmenrtfromthegel.2d��21����������������������������������������;>/B3��dCHAPTER2. #REFERENCEdd[cDDmanrualr�rGn2.4-CTheConstrainrtsWindow7pTheI]\Constraints"windorwdisplaysalistofcurrentlyassertedconstraints,a togetherwithUMamenrubarwithbuttonslabSeled\Add",\Drop",and\Negate".3Itprovideswaystochangethe3existingconstrainrtsandaddnewones.>Eachconstraintislistedasonelineoftextinthe\Constraints"windorw.8EachconstraintisalsoanactivebuttonwithapSopupmenu."ʫ2.4.12Constrain=tsMEacrh-constraintappSearsasastatementgivingaconstraintrelationshipbSetweenasingledigestKfragmenrtandadoubledigestfragment.Z%ClickingonaconstraintbringsupapSopupmenruthatallowsyoutodropornegatethatconstraint.2.4.1.13�Drop.ChoSosingthisremorvestheconstrainrt.2.4.1.23�Negate�(Un-Negate).ChoSosingthistransformstheconstrainrttoitsopposite.8\identical"becomesUM\not-identical", andjcsoon.ThiscrhoiceappSearsas\Un-Negate"iftheconstraintisinthenegativreform."ʫ2.4.22AddClicrkingonthisbuttoncausesapSopupmenutoappSearthatlistssixpossiblekindsofconstrainrtkeyoucanimpSoseonyourdata.EachconstraintdescribSesarelationshipbetrweentrwofragments,oneofwhichmustbSeasingledigestfragmentandtheotheradoubledigestfragmenrt.<AllpSossibleconstraintchoicesareassertedinthesamewayV.<ChoSosetheconstraintbrym clickingonyourchoicefromthe\Add"menu.GClickonthe rstbandintheconstraintrelationship,+:thenPclicrkonthesecondone.Theorderinwhichyouclickmakesadi erencefor! constrainrtsotherthanidenticalornot-identical,I_soitisagoSod! ideatoloSokinthewindowafterimpSosingaconstrainrttobesureDDgotitrighrt.2.4.2.13�Iden�tical.ChoSosethistoassertthatyrourfragmentisidenticalwithanotherfragment.2.4.2.23�Not�Iden�tical.ChoSosethistoassertthattrwofragmentsarenotidentical.2d��22����������������������������������������F /B3��dCHAPTER2. #REFERENCEdd[cDDmanrualr�rGn2.4.2.33�Bigger�Than.MChoSosethistoassertthatthefragmenrtyouclickedonisbiggerthananotherfragment.2.4.2.43�Smaller�Than.ChoSosethistoassertthatthefragmenrtyouclickedonissmallerthananotherfragment.2.4.2.53�Con�tains�(PartOf:).ChoSoseދthistoassertthatthesingledigestfragmenrtyouclickedoncontainsaparticularUMdouble-digestfragmenrt.wIfyouclickedonabandinthedoubledigestlane,>thismenuitemreads\Part,of".2.4.2.63�Not�Con�tains(NotPartof:).MChoSose>thistoassertthatthesingledigestfragmenrtyouclickedondoSesnotcontainaparticularpdoubledigestfragmenrt.Ifyouclickedonabandinthedoubledigestlane,;thismenruitemreads\Not,Partof"."ʫ2.4.32DropDropaconstrainrt.Clickonthe\Drop"button,Pthenclicrkontheconstraintyouwanttodrop."ʫ2.4.42NegateNegate]aconstrainrt.Click]onthe\Negate"button,z`thenclicrkontheconstraintyouwanttonegate.(V2.5-CMaps7pThe\Maps"windorwdisplaystherestrictionmapsDDmakes. Itdisplaysthemintext,linear,ZtandDcircularforminwraysDthatyroucancontrol.E/Therearebuttonsacrossthemenubar,labSeledp\Make,Maps",\Configure",and\Save".xThewindorwitselfhastwobuttonsatthetoplabSeled\Next"and\Prev",whicrhallowyoutopagethroughmultiplemaps.&?BelowtheseO8buttonsisalinethatsaryshowmanymapsareinthesetandwhichoneiscurrentlydisplaryed.ItalsoshorwsthegoSodnessof toftermsofthe%ofmaximumdeviationallowedfortheerrorrangescrhosen.BelowthatisalineinsmallprinrtthatdescribSeswhichfragmentsarexunordered.zTherestofthewindorwcontainsatextmaptogetherwithalinearand/orcircular>map.ThetextmapshorwsfragmentslabSeledbytheirsizes,withverticallinesforcutSsites,qanddoublevrerticallinesforcoincidentcutsites.UnorderedfragmentsaregroupSedbryahorizontalline.",Thelinearandcircularmapseachhavethreelines,+oneforeachdigest.2d��23����������������������������������������O͠/B3��dCHAPTER2. #REFERENCEdd[cDDmanrualr�rGnThedoubledigestisinthecenrter,�FandrestrictionsitesarelabSeledbyverticaltics.lPuttingUMthepSoinrteroverafragmentcausesinformationabSoutthatfragmenttoappSearinthewindow."ʫ2.5.12Mak=eMapsMClicrkmonthisbuttontotellDDmtocomputemaps.=Theprogressofthecomputationisshowninthetopwindorw.6TherearetwokindsofwarningbSoxesthatmaycomeupafteryouclickonz'\Make,Maps".\OnewrarnsabSoutinconsistencyinthedata,andanotherwarnsthattheproblemiscomputationallydicult.2.5.1.13�NOTE,�W�ARNINGorERR�ORconcerningyourdata.DDcrheckseverydatasetforinternalconsistencybSeforecomputingmaps.&Ifyouenterdatagraphicallyanddonotselect\Critique,CurrentData"fromthe\Other"menru,-CDDwilldoitautomaticallywhenyrouclickon\Make,Maps".1@DDwillcheckthatalllanesadduptothesamemolecularwreight(withinerrorlimits).DDwillalsocounrtfragmentsinthedoubledigestlanecomparedtothesingledigestlanesandtellyrouifthefragmentnumbSerslookstrangeSorsuggestlinearorcircularDNA.Afteryrouhavereadthecritique,dclickon\Stop,toReview,Data"4Oifyrouwanttoedityourdata,Xorclickon\Continue,withCurrentData"4Otomakre{]mapsanywayV.Thelatteroptionisnoto eredincaseoferror(e.g.whennofragmenrtsharvebSeenenrteredinoneofthelanes).2.5.1.23�W�ARNING:�Thislo`�okslik�eahardproblem.ThisvwrarningmeansthatDDuislikelyto ndhundredsorthousandsofmaps.ChoSose\Stopto,AddConstraints"ǽtoabSortthecomputationand\Continue,Computing"toconrtinueit.GUsually+itiswisetocrhoSose\Stop,toAddConstraints".Not+onlywillDD+harve+troublewithltheproblem,4buttheanswrerwillnotbSeveryusefulanywayV.IfthisbSoxappSears,4itcouldmeanJthatyrouneedtoaddconstraints.0Itcouldalsomeanthatyourdataisfundamentallyamrbiguous.8Inthatcase,doanotherexpSeriment!Caution.ChoSosing\Continue,Computing"afterthiswrarningcanmakeDDrunoutofmemoryandcrash.8IfyrouwishtochoSosethis,saveyourdataandmaps rst."ʫ2.5.22Con gureClicrking&onthisbuttonmakesapSopupmenuappSearthatallowsyoutocontroltheformatofdisplaryedmaps,theformatofmapssavedto les,andwhichdoubledigestfragmentisdisplaryedattheleftendofalinearmaporat12o'cloScrkonacircularmap.2.5.2.13�Change�MapDispla�yF�ormat.ChoSosethistocrhangetheformatwithwhichmapsaredisplayedinthe\Maps"window.2d��24����������������������������������������Z/B3��dCHAPTER2. #REFERENCEdd[cDDmanrualr�rGnT�ext�andLinearOnly. DisplarytextandlinearmapsonlyV.T�ext�andCircularOnly. DisplarytextandcircularmapsonlyV.T�ext,�Linear,andCircular. Displaryallthreemapformats.2.5.2.23�Change�MapFileOutputSt�yle.MChoSosing,EthisbringsupadialogborxthatyoucanusetocontroltheformatwithwhichmapsUMarexsarvedtodisk.OThecurrentsettingfor leformatisshowninheavyblack.OBelowitarethreeB<buttonsforyrourpSossiblechoices.?ClicktochoSose.?YVoucansaveyourmapasASCISItext,pSostscriptgraphics,orpSostscripttext.IfyrouaresavingyourmapsinpSostscript,youcanralsocrhoSosewhethertosaveitinmonoSchromeorcolor.6yWhenyouarehappywithyourcrhoices,clickon\SET,FORMAT".Clickon\CANCEL"toleavethesesettingsastheywere.2.5.2.33�Anc�hor�aDoubleDigestF�ragmentinLeft/12-O'Clo`�ckPosition.ChoSosingsthisallorwsyoutochoSosethe rstdoubledigestfragmentdisplayedonthemap,startingattheleftendorcloScrkwisefrom12o'clocrk.$OApopupmenruwillappearlistingyrourdoubledigestfragmenrts.8Clickontheoneyrouwant."ʫ2.5.32Sa=veChoSosethisbuttontosarveoneormoremapstoa leortocrhangetheformatinwhichmaps\aresarved. With\theexceptionofcrhoSosinga leformat,y allofthesubtopicsherefollowexactlykthoseunderthe\Save"buttoninthe\Digest,Data"windorw.See2.3.2fordetailedheadings.2.5.3.13�Change�MapFileOutputSt�yle.ChoSosing,Ethisbringsupadialogborxthatyoucanusetocontroltheformatwithwhichmapsarexsarvedtodisk.OThecurrentsettingfor leformatisshowninheavyblack.OBelowitarethreeB<buttonsforyrourpSossiblechoices.?ClicktochoSose.?YVoucansaveyourmapasASCISItext,pSostscriptgraphics,orpSostscripttext.IfyrouaresavingyourmapsinpSostscript,youcanralsocrhoSosewhethertosaveitinmonoSchromeorcolor.6yWhenyouarehappywithyourcrhoices,clickon\SET,FORMAT".Clickon\CANCEL"toleavethesesettingsastheywere.2.5.3.23�Sa�ve�AllMapstoFile.ChoSosethistosarveallofthemapsyroumadeforthecurrentlyselecteddigesttoa le.FVoradiscussionofoptionsforsarvingto le,seesection2.3.2.2d��25����������������������������������������fʠ/B3��dCHAPTER2. #REFERENCEdd[cDDmanrualr�rGn2.5.3.33�Sa�ve�CurrentMaptoFile.MChoSosek!thistosarvek!thecurrenrtmaptoa le.^YVoucanputitinaneworexisting le.FVoranUMexisting le,yroucanappSendthemaporreplacethecontentsofthe lewiththenewmap.FVoradiscussionofoptionsforsarvingto le,seesection2.3.2.(V2.6-CMatcrhDetails7pThis@ isanoptionalwindorw.�ItshowsdetailsofthecalculationsthatDD?makesto ndmaps.ItalhasamenrubaracrossthetopwithbuttonslabSeled\Possibilities",\Constraints",\Compatibility",\Sets",\Maps",andz\Close,Window". R\CloseWindow"remorvesthe\Match,Details"wwwindorw. NEachoftheotherbuttonstellsDDwtotakeitsmapmakingcalculationҽtotheparticularstagedescribSedbrythatbutton(seebelorw). Therearethreesubrwindowsˡinthemainwindorw..ThetoptwolistthenumbSerofpossibilitiesDD˙isconsid-ering=6foreacrhenzymeonafragmentbyfragmentbasisateachstageofthecalculation.EachnrumbSerWofpossibilitiesisitselfabutton.pClicrkingonitcausesthepossiblematcrhestoappearinKathirdsubrwindowKatthebSottom.\dPlacingthepoinrterononeofthesepossiblematcrhescausesfurtherinformationtoappSearonthetopsubrwindowofthemainDDwindorw.WVebrie youtlinehorwDDmakesitscalculations,notinginparenthesesthenameofthebuttonUthattakresDDtothatparticularstage.DD rstcalculatesallpSossiblewraysUthateacrhfysingledigestfragmentcanbSebuiltupfromcombinationsofdoubledigestfragments,allorwingforbSoththecurrenterrorrangesandthepSossibilityofsmallundetectedfragments(\Possibilities").LInF_thenextstep,]MDDFGeliminatesanryofthesethatarenotcompatiblewithconstrainrtsthatyouimpSosed(\Constraints").Next,1DDeliminateswaysofbuild-ingtsingledigestfragmenrtsfromdoubledigestfragmentsthatareinternallyinconsistent(\Compatibility").FVorlexample,ifaparticulardoubledigestfragmenrtisalwaysneededtobuildoneofthesingle-enzymefragmenrts,0nootherfragmentfromthesamesingle-enzymelanecouldbSebuiltusingthatdouble-digestfragmenrt.XInternallyconsistentsetsarethenconstructedforeacrhsingle-digestlane,Z-usingeachdoubledigestfragmentonce(\Sets").FinallyV,thesesetsaremergedtoformsummarymaps(\Maps").FVorfurtherdetails,conrtacttheprogram'sauthordirectly(detailsatendofmanual).2d��26����������������������������������������r@/B3nHChapter 32��Installation andIn4ternals6UMDDiswrittenintheCommonLispprogramminglanguage.'ThegraphicalinrterfaceusesUMtheCommonLispInrterfaceManager(CLIM),anemergingstandardforpSortablegraphicssuppSorted2bryallthema�jorCommonLispvendors. yItshouldbSefairlyeasytocon gureandrunDDwonanrycomputerforwhichCommonLispandCLIMwareavXailable.oCLIMwiscurrenrtlyavXailableforX11,Macintosh,MicrosoftWindowsandGenerasystems.InYkpractice,uwrehavebSeendevelopingandtestingitontwosystems:eMacintoshesusingMacinrtoshϲCommonLispandCLIM,andSunSparcstationsusingLucidCommonLispandCLIM..Thecon gurationsusedfordevrelopment.andtestingareindicatedbSelorw;Wduetothemanry?pSossiblevXariationsinhardwareandsoftware,wecanonlysaywedonotyethaverepSorts8`ofmodels,Kwindorwmanagers,etc." withwhicrhDD8Lwon'twork." ThoseinterestedinrunningitonothercomputersystemsshouldconrtactusdirectlyV.(V3.1-CMacinrtosh#3.1.12InstallationMIf|yrouobtainedacopyofDDAwhose lenameendsin\.hqx", 1youneedto\unbinhex"it,usingoneoftheprograms(sucrhasCompactProorStut)whichdothis.!TheresultwillbSe a leendingin\.sea",�bshortforselfextractingarcrhive.mClick onthis le,anditwillaskyroutospSecifyadestinationfolderinwhichtoextractthearchive'scontents.dzClickingon\Extract"willcreatea\DoubleDigester"folderintheloScationyrouselected.&Inthisfolderyrouwill ndtheapplication,n\DoubleDigester",andafoldercalled\data",conrtaining leswithsampledoubledigestandgelstandarddata.ThekDDkdapplicationoSccupiesabout2.8MBkdofdiskspace,andrequiresabout5MBkdofmemorytorun.IfyrougiveDDnmorememory(using\Get,Info"fromthe\File"menutokBcrhangethe\Current,size"settingbSeforeyourunDD),itwillbSeabletodealwithmore and/orharderdigestsbSeforeitrunsoutofmemoryV./IfthisrequiresrunninginvirtualmemoryV,yhorwever,DD٨willrunvrerymuchslowerthanifitcanrunentirelyinbuilt-inmemory(select\About,ThisMacintosh"fromtheAppleMenruto ndoutabSoutyourmachine).2��27����������������������������������������~+/B3��dCHAPTER3. #INSTVALLATIONANDINTERNALSdd[cDDmanrualr�rGnWhenZDDstartsup,1itloSoksinthefolderfromwhicrhitstartedforafoldernamed\data";UMit/willuseeitherthisoritsstartupfolderasthedefaultfolderforreadingandwriting les(thisisresetablefromthe\Configure"menru).IfvyrousavemapsinpSostscriptformat,٪youwillneedtoprintthemusingaprogramwhicrhwcansendpSostscript lestoaprinter.NFVorSystem7,youcanusethe\LaserWVriterUtilitry"Mthatcomeswithit,lbyselectingthe\Download,PostscriptFile:::k"Moptionfromthe\Utilities"menru.8FVorSystem6,youwillneedaprogramsuchas\SendPS"."ʫ3.1.22TroubleshouotingMIf`DD isunrespSonsivre,!andisnotinthemiddleofcalculatingorsavingmaps,!itmaybSewraitingEforinput.YVoucanselect\Windows"fromtheMacintoshmenubartoseeifthereareanrypSopupwindowswhichmayhavebSecomeburied,,andcheckthetopwindowforanrycmessagesindicatingDDbiswaitingforsomething.6AlternativelyV,youcansimplyhitthe\Command-."ykreycombinationtoabSortanypSendingprocessandreturntonormalinrteraction;thisisalwrayssafetotryV.ThecurrenrtversionofDDhasbSeentestedonthefollowingtypSesofMacintosh:MacISIx,MacISIfx,QuadraUFandProwerBook. xItUFhasrunonmonocrhrome,grayscaleUFand8-bitcolordisplarys.IDDarunsaunderbSothSystem6andSystem7.IfyrouhaveproblemswithnormalrunningUofDD,tryrunningitwithoutanrydeskaccessoriesactive(wedonotknowofanycon icts,butthisisacommonsourceofproblemsontheMacinrtosh).(V3.2-CUnixandX11#3.2.12InstallationIf1:yrouobtainedacopyofDD1 whose lenameendsin\.tar.Z",youwillneedto\uncompress"itandthenextracttheconrtentsoftheresultingtar le.8Thesimplestwraytodothisis:UM1fhzcat,double-digester.tar.Z|tarxvf-whicrhwillcreateadirectorycalledsomethinglike\dd-1.1",containingtheapplicationUM\double-digester"anda\data"directorywithsampledoubledigestandgelstandarddata.TheHDDapplicationoSccupiesabout12MBofdiskspace,andusesabout24MBofmemory(phrysical}orswap)torun.4YVouwillprobablyneedatleast40MBzofswapspace,preferably50K"MBJormore,k toallorwforwindowingandothersoftwareonyoursystem.IfyouneedmoreswrapWspace,4youoryoursystemadministratormightwanttoconsiderusingswap lesasanalternativretorecon guringdisks(cf.8manpagesonmk leandswapSon).WhenDDstartsup,itloSoksinyrourcurrentworkingdirectoryforasubSdirectorynamed\data";y}itIwilluseeitherthisoryrourcurrentdirectoryasthedefaultdirectoryforreadingandwriting les(thisisresetablefromthe\Con gure"menru).2d��28����������������������������������������/B3��dCHAPTER3. #INSTVALLATIONANDINTERNALSdd[cDDmanrualr�rGn3.2.22TroubleshouotingMIf`DD isunrespSonsivre,!andisnotinthemiddleofcalculatingorsavingmaps,!itmaybSeUMwraiting|forinput.-YVoucanloSoktoseeifthereareanydialogbSoxesormenusaround(menusunderX11shoulddisappSearwhenburied),andcrheckthetopwindorwforanymessagesindicatingDDbiswraitingforsomething.YVoucannexttryhittingtheinterruptkey(often\Control-C")to abSortanrypendingprocessandreturntonormalinrteraction;>thisisalwayssafetotrysolongaskreybSoardinputisdirectedtotheDDwindow._IfthisdoSesn'tworkoryrouSwanttoterminatealongcomputation,dyoucandirectittothewindowfromwhichyoustartedDD,andthencrhoSoseanappropriaterestartoption(normally\:A"orthenumbSer{probably\2"or\5"{precedingthewrords\Double,Digestertoplevel").AppropriaterkreybSoardinputtoDDrisalwaysdirectedtoadialogbSox,notthemainwindorw.|5Nevertheless,qaifVoyoudotypSeatthekeybSoardandpress\return"whentheinputfoScus isdirectedtothemainwindorwofDD,thelinetypSedatthekeybSoardwillsometimesappSearatthetopleft,orverthemenrubarofthemainwindow.6Whentheline rstappSears,the\qmacrhinebSeeps.;WhenthepoinrterismovedacrosstheDD\Tmainwindow,xthetextwilldisappSear.Itwillreappearagainwhenthewindorwisresized,>butvXanishagainwhenthepSoinrter^ismoved. NThisisabug.MorvingthepSointerisamuchmorecommonopSerationthanresizing,andhenceitiseasytowrorkaroundthisproblem.TheNecurrenrtversionofDDNKhasbSeentestedonaSunSparcstationIINKrunningOpenWin-dorws\3.0with32MB(ofmemoryV,G8andonaSparcstationELCwith24MBofmemoryrunningOpSenWindorwsG2.0.PRemotedisplayonaHP9000/370workstationusingtheMotifwindowmanager, andbonaMacinrtoshrunningaMacXUserver, hasalsobSeentested.'AUpreviousver-sionwrasalsobuiltandrunonanHP9000/370with16MBofmemoryV,husingLucidCommonLispandCLIMunderX11R4withMotif.(V3.3-CAllVXersions#3.3.12ErrorReco=veryIfSDDrunsoutofmemoryorencounrterssomeotherseriousproblem,=itshouldprovideawrarningthatithashitaninternalerror.@9Itgivesacountdownofhowmanymoretimesitwillattempttorecorver,^toavoidin niteloSops,^andthenattemptstoreturntoastatewhicrhkallowsyoutosaveyourdataandmaps.(Besuretoimmediatelysaveanydataandmapsd(probablybSestinthatorder)whicrhareimportanrttoyou:XwhileyoumightbSeabletocconrtinueworkingnormallyV,problemssuchasrunningoutofmemoryarelikelytorecursoSon."ʫ3.3.22MemoryManagemen=tDDa4freesamemorywhenevreritcan. ThisproScessiscalled\garbagecollection".OntheMac,!itishappSeningwhenevrertheusualcursordisappearsandisreplacedwitha\GC"2d��29����������������������������������������/B3��dCHAPTER3. #INSTVALLATIONANDINTERNALSdd[cDDmanrualr�rGncursor.OntheSun,DDprinrtsamessageinthewindowitwasstartedfromthatbSeginsUM\;;;,GC:".Withtrypicalproblemsthatdonotelicitacomplexitywarning(see2.5.1.2),DD-should6alwrayshaveplentyofmemoryV.ThereisonepSossibleexceptiontothis:DD-canrun@AoutofmemoryifalargeenoughnrumbSer@Aofdatasetsaremapped.9ThereasonforthisisthatDDsarvesallrelevXanrtinformationforeachdataset,includingconstraints,allerrorinformation,andinrtermediateresults.HThisallowsyoutoswitchbSetweendatasetswithoutharving$0torecalculateresults,2butitalsomeansthatDD$"tendsto llupitsmemoryasyouuseitrepSeatedlyV.rIfgarbagecollectionisbeginningtooccurfrequenrtlyV,%saveyourdataandmaps[andrestartDD.WhenDD[sarves[adataset,xEitsarves[allstandards,constrainrtanderrorinformation,soyroucanregenerateallmapsfromsaveddata."ʫ3.3.32Sa=vingLargeMapFilesMIf yrousavemapsinpSostscriptformat,theycanuselargeamountsofspace.DD warnsyouabSoutMthisifyrouselectthepostscriptoutputoptionwithmorethan10maps,#butdoesnotdosovotherwise,nordoSesitattemptto ndoutwhetherenoughspaceexiststowritethemout.If?yrouwanttocheckhowmuchdiskspaceasetofmapswilltake,asimplychoSosethe\ChangeMap,FileOutputStyle"3JoptionontheMaps\Save"menru,WandreselectpSostscriptoutput.(V3.4-CFXurtherInformationandSuggestions7pFVorBadditionalinformation,$torepSortbugs,ortosuggestthingsyrouwouldliketoseeincludedorcrhanged,contactDD'sauthor:UM1fhLawrence,Wright1fhMedical,InformaticsCenter1fh3,TMP-Anesthesiology1fhYale,SchoolofMedicine1fhNew,Haven,CT06510-33331fhPhone:,(203)7857453,78528021fhFAX:g(203),7372243,78566641fhINTERNET:,wright-lawrence@yale.edu1fhBITNET:gwright-lawrence@yalecs.bitnet1fhUUCP:yale!wright-lawrence2d��30�Z;����/G� �H"V�G� ���cmbx10BK`y�G� ���cmr10<"V�G� ���cmbx107"V�ff� ���cmbx105 b>�ff� ���cmmi104K`y�ff� ���cmr101߆T� ��� ���cmtt120N� ��� ���cmbx12/}h!� ��� ���cmsl12.@� ��� ���cmti12,g� ��� ���cmmi12+XQ � ��� ���cmr12�0