Downloaded from httpsacademicoupcombioinformaticsarticleabstract331421973072872by University of Arizona useron 28 February 2018 CoGehasdevelopedtwonewwebbasedtoolsthatcomplementitsexistin ID: 844303
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Downloaded from https://academic.oup.com/bioinformatics/article-abstract/33/14/2197/3072872by University of Arizona useron 28 February 2018 Downloaded from https://academic.oup.com/bioinformatics/article-abstract/33/14/2197/3072872by University of Arizona useron 28 February 2018 CoGehasdevelopedtwonewweb-basedtoolsthatcomplementitsexistingtoolsforwholegenomeandmicro-syntenyanalyses,SynMap2andSynMap3D.Bothtoolsvisualizesyntenyacrosswholegenomesusingdot-plots,andillustratemutationratepatternsthroughcolor-mappedhistograms.SynMap2(SupplementaryFig.S1A)isadynamic,interactive,high-performanceweb-basedvisual-izerforcomparingtwowholegenomes,andboastsmanynewfeaturesandperformancebenefitsovertheoriginalSynMap(etal.,2008).SynMap3D(SupplementaryFig.1B)isanovel,3Dsyn-tenyviewerthatidentifiessyntenycommonamongthreegenomes.2.1SynMap2SynMap2isamajorreworkingoftheoriginalSynMappairwisewhole-genomesyntenyviewer.ItprovidesanumberofbenefitsovertheoriginalSynMaptoolbyreplacingstaticimageswithahighper-formanceandinteractiveweb-baseddot-plotviewer.SynMap2sinteractivefeaturesallowresearcherstoexplorethedatasetfrommultipleangleswithoutrequiringadditionalknowledgeofdatabasequerylanguages.Subsetsofsyntenicmatchescanbeselectedbychromosomalregionsorbysubsetrangesofmutationvalues(Kn,KsorKn/Ks).Assubsetsareselected,thevisualizationisautomatic-allyupdated.Thesubsetselectionalgorithmsaredesignedtoworkefficientlyandarebuiltupontheopen-sourceprojectCrossfilter(http://square.github.io/crossfilter/),afastdatastructureforincre-mentaldataqueryingandaggregation.SynMap2sdot-plotsarevisualizedas2Dscatterplots.VisualsaregeneratedthroughacombinationofD3(https://d3js.org/),SVGDahlstroetal.,2011),andacustomimplementationofthedatapointsusingHTML5Canvas(etal.,2015).ThiscustomimplementationavoidstheoverheadofkeepingindividualdatapointsintheDocumentObjectModel.Dotsarecoloredbasedontheirmutationratiosusingadata-drivencolormapdesignedtosplitthehistogramofmutationvaluesintoclusters,suchthatclustersofsimilarvaluesaregivensimilarcolors.Atechniquefromcomputa-tionaltopologyknownaspersistence-basedsimplificationisusedtoidentifythemostimportantpeaksinthehistogramtogeneratethesecolormaps(EdelsbrunnerandHarer,2010).Coordinatingthecolorsbetweenthehistogramanddot-plotillustratesgenome-widepatterns(e.g.polyploidy)andhighlightsgenomicregionswithdifferentdriftratiosandevolutionaryorigins(e.g.lineagediver-gence).AnumberofexampleSynMap2analysescanbefoundinSupplementaryTableS1.2.2SynMap3DSynMap3DisanoveladditiontotheCoGetoolboxdesignedtocompareandvisualizewhole-genomesyntenyacrossthreegenomesinaninteractive,threedimensionaldot-plot.SynMap3Dallowsre-searcherstospecifythreegenomes,andusesCoGescomputationalpipelinestodynamicallyidenti
2 fysyntenygenesetsamongallthreegenomes.Th
fysyntenygenesetsamongallthreegenomes.Theresultsaredisplayedtotheuserintheformofa3Dscatterplot.Visualizationsarerenderedthroughtheopen-sourcetechnologiesD3andThree.js(http://threejs.org/),withmodifica-tionstoenhanceperformanceandprovideintuitiveinteractionwiththedata.Interactivefeaturesandcolor-mappedhistogramofmuta-tionvaluesissimilartoSynMap2.SynMap3Dalsoincludestheop-tiontoenablevirtualreality(VR)mode,allowingresearcherswithaVRheadsettointeractwiththeirdatainanimmersive,responsiveenvironment.TotakeadvantageofVRmode,usersmusthaveaVR-compatiblebrowserandVR-headset(e.g.OculusRift).Anum-berofexampleSynMap3DanalysescanbefoundinSupplementaryTableS2.3AvailabilityandrequirementsBothtoolsareavailableonlinethroughCoGe(http://www.genomevolution.org).BothrequireamodernHTML5capablebrowser,andSynMap3DrequiresWebGLbeenabled.VRmodeinSynMap3Dre-quiresaVR-compatiblebrowser(MozillaFirefoxorGoogleChrome)andaVRheadset.UserscanvisualizeanyofCoGespubli-callyavailablegenomeswithoutcreatingauseraccount,butmustregistertouploadtheirowngenomesoraccessrestricteddata.Moredetaileduseinstructions,help,andexampleanalysesforareavail-ableoneachtoolsrespectiveCoGePediapage(https://genomevolution.org/wiki/index.php/SynMap3Dandhttps://genomevolution.org/wiki/index.php/SynMap2).AcknowledgementsWewouldliketothankCyVerse(formerlyiPlant)forsharingbestpracticesandprovidingdataandcomputationalinfrastructureforCoGe(NSFDBI1265383),andthecontributorstoD3andThree.jstheirrolesindevelopingandtestingpowerfulwebvisualizationframeworks.ThisworkhasbeensupportedbytheNationalScienceFoundationgrants[IOS1339156andIOS1444490].ConßictofInterest:nonedeclared.Cabanier,R.etal.(2015)HTMLCanvas2DContext.WorldWideWebConsortium.¨m,E.etal.(2011)ScalableVectorGraphics(SVG)1.1,2ndedn.WorldWideWebConsortium.Edelsbrunner,H.andHarer,J.(2010)Computationaltopology:anintroduc-Am.Math.SocKrzywinski,M.I.etal.(2009)Circos:Aninformationaestheticforcompara-tivegenomics.GenomeRes,16391645.Lyons,E.andFreeling,M.(2008)HowtousefullycomparehomologousplantgenesandchromosomesasDNAsequences.PlantJ,661673.etal.(2008)ThevalueofnonmodelgenomesandanexampleusingSynMapwithinCoGetodissectthehexaploidythatpredatestherosids.Trop.PlantBiol,181190.McKay,S.J.etal.(2010)UsingtheGenericSyntenyBrowser(GBrowse_syn).Curr.Protoc.Bioinformatics,Chapter9:Unit9.12. A.Haug-Baltzelletal. GenomeanalysisSynMap2andSynMap3D:web-basedwhole-genomesyntenybrowsersAsherHaug-Baltzell,SeanA.Stephens,SeanDavey,CarlosE.ScheideggerandEricLyonsGeneticsGIDP,DepartmentofComputerScienceandBIO5Institute,SchoolofPlantSciences,UniversityofArizona,TucsonAZ85721,USA Bioinformatics,33(14),2017,21972198doi:10.1093/bioinformatics/btx144AdvanceAccessPublicationDate:16March2017ApplicationsNote