生信网站

NucleicAcidsResearch,2017,Vol.45,WebServerissueW1鈥揥5doi:10.1093/nar/gkx457Editorial:the15thannualNucleicAcidsResearchWebServerissue2017The2017WebServerissueofNucleicAcidsResearchisthe15thinaseriesofannualissuesdedicatedtoweb-basedsoftwareresourcesforanalysisandvisualizationofmolecularbiologydata.ItisfreelyavailableonlineunderNAR鈥檚openaccesspolicy.Thisyear,284proposalsweresubmittedand102,or36%,wereapprovedformanuscriptsubmission.Ofthoseapproved,86,or84%,wereultimatelyacceptedforpublication.Table1liststhe2017WebServers,theirURLs,andabriefdescriptionofeach.Topics.ThepapersintheWebServerIssuereflectcurrentandemergingtrendsincomputationalbiologyresearch.Ofpar-ticularnotethisyearareseveralwebsitesdealingwithbiosyntheticgeneclusters(BGCs)inbacteria,fungi,andplants.Thepotentiallyusefulsecondarymetabolitesornaturalproductsproducedbythesegeneclustersincludenovelantibiotics,polyketides(PKs),nonribosomalpeptides(NRPs),andribosomallysynthesizedandposttranslationallymodifiedpeptides(RiPPs).ThewebsitesusegenomeminingtoidentifyBGCs,predictthestructuresofthemetabolites,oridentifyBGCswhichproducemetaboliteswithchemicalstructuressimilartoaquerycompound.Sevenpapersdealwiththesetopics:antiSMASH4.0,ARTS,plantiSMASH,PRISM3,RiPPMiner,SBSPKSv2andSeMPI.Otherpapersinthisyear鈥檚issuefallintothefollowingbroadcategories:(i)geneexpressionandenrichmentanalysis,(ii)pre-dictionoffunctionalandstructuraleffectsofmutations,(iii)proteinstructure,binding,anddocking,(iv)datavisualizationsand(v)miscellaneoustopics.Thegeneexpressioncategorycontainseightpapers,including:agriGOv2,anupdatewhichprovidesGOenrichmentanalysisinplants,GEPIA,atoolforgeneexpressionandsurvivalanalysisincancerdatasets,WebGestalt,anupdateonapopularcollectionoftoolsforgenesetfunctionalenrichment,andWoPPER,whichdetectsbacterialchromosomeregionswhichexhibitcoordinatedgeneexpressionchanges.Themutationaleffectscategorycontainstenpapers,includingGenProBiS,whichmapsvariantstoproteinbindingsitesandallowsinspectionoftheinteractionwithboundligands,mCSM-NA,whichpredictstheeffectofproteinmutationsonnucleicacidbindingaffinities,andmTCTScan,whichprioritizesmutationsthatwillaffectcancerdrugresponse.Theproteinstructureandbindingcategorycontains18papers,including:DynOmics,formoleculardynamicssimulationsusingelasticnetworkmodels,LigParGen,whichgeneratesmoleculardynamicsforcefieldparametersfororganicligands,ModFOLD6,anupdatewhichprovidesqualityassessmentforprotein3Dmodels,ReFOLD,whichrefinesprotein3Dmodels,andTRAPP,whichdetectstransientbindingpocketsthatarisefrominternalproteinmotion.Thedatavisualizationcategorycontainssevenpapers,including:BioAtlas,forvisualizingmicrobialtaxadistributionsbothgeographicallyandonthehumanbody,DSSR,whichaddssupportforRNA3Dstructure,includingbasepairs,doublehelicesandhairpinloops,totheJSmol/Jmolbiomolecularstructurevisualizationsoftware,kpLogo,whichdetectsultra-shortsequencemotifsfromamultiplealignmentandshows,ateachalignmentposition,themostsignificantstartingk-mer,MutaGene,forvisualizingcancermutationalprofiles,andWeb3DMol,forprotein3Dstructurevisualization.Thelargemiscellaneouscategoryincludes:IslandViewer4.0,anupdatewhichdetectsbacterialhorizontalgenetransfer,SLiMSearch,anupdatewhichscansproteomesfornewinstancesofshortlinearmotifs(SLiMs),occurringinproteindisor-deredregions,andprovidesavarietyofannotationandfilteringoptions,ProteoSign,anapplicationforproteindifferentialabundanceanalysisusingmassspectrometrydata,compleXView,whichinfersproteincomplexesusingmassspectrometreyabundanceandproteincontactdata,BAR3.0,andCOFACTOR,bothupdates,whichprovideproteinfunctionannotation,IntaRNA2.0,anupdatewhichpredictsandanalyzesRNA-RNAinteractions,RNA-MoIP,forpredictingRNA2Dand3Dstructures,andSpartaABC,asequencegenerationtoolwhichincorporatesindels.Stand-aloneprogramsandwebservices.TheWebServerissueadditionallyhasspecialsectionsforstand-alonetoolsforhigh-throughputdataanalysis,whichmustbeinstalledontheresearcher鈥檚computer,andwebservicesfordataandanalysis,whichareaccessedprogrammaticallyratherthanbymanualinteractionwithawebsite.Threepapersreportonlargecol-C漏TheAuthor(s)2017.PublishedbyOxfordUniversityPressonbehalfofNucleicAcidsResearch.ThisisanOpenAccessarticledistributedunderthetermsoftheCreativeCommonsAttributionLicense(http://creativecommons.org/licenses/by/4.0/),whichpermitsunrestrictedreuse,distribution,andreproductioninanymedium,providedtheoriginalworkisproperlycited.Downloadedfromhttps://academic.oup.com/nar/article-abstract/45/W1/W1/3896331/Editorial-the-15th-annual-Nucleic-Acids-ResearchbyShantouUniversityuseron16October2017W2NucleicAcidsResearch,2017,Vol.45,WebServerissueTable1.DescriptionsofwebserversintheNAR2017WebServerissueWebServernameURLBriefdescriptionagriGOv2http://systemsbiology.cau.edu.cn/agriGOv2/GOanalysisforagriculturalspeciesAMMOS2http://drugmod.rpbs.univ-paris-diderot.fr/ammosHome.phpEnergyminimizationofprotein鈥搇igandcomplexesantiSMASHhttp://antismash.secondarymetabolites.org/SecondarymetabolitebiosyntheticgeneclustermininginbacterialandfungalgenomesARTShttp://arts.ziemertlab.comBiosyntheticgeneclusterminingfornovelantibioticsBAR3.0http://bar.biocomp.unibo.it/bar3ProteinstructureandfunctionannotationBepiPred-2.0http://www.cbs.dtu.dk/services/BepiPred-2.0/B-cellepitopepredictionfromaproteinsequenceBioAtlashttp://bioatlas.compbio.sdu.dkVisualizationofmicrobiomeandmetagenomelocationsBIS2Analyzerhttp://www.lcqb.upmc.fr/BIS2Analyzer/Analysisofcoevolvingamino-acidpairsinproteinsequencesBusyBeehttps://ccb-microbe.cs.uni-saarland.de/busybeeMetagenomebinningCAFEhttps://github.com/younglululu/CAFEStand-aloneprogramforalignment-freecomparisonofmetagenomedataCancerPanorOmicshttp://panoromics.irbbarcelona.orgMappingofcancermutationsto3Dprotein鈥損roteininteractionsitesCOFACTORhttp://zhanglab.ccmb.med.umich.edu/COFACTOR/Structure-basedproteinfunctionannotationcompleXViewhttp://xvis.genzentrum.lmu.de/compleXViewProtein-proteininteractionbasedonaffinitypurificationmassspectrometryConTrav3http://bioit2.irc.ugent.be/contra/v3TranscriptionfactorbindingsitesanalysisCPC2http://cpc2.cbi.pku.edu.cnProteincodingpotentialofRNAtranscriptsCSPADEhttp://cspade.fimm.fi/ChemoinformaticsbioactivityassayvisualizationCSTEAhttp://comp-sysbio.org/cstea/Analysisoftime-seriesgeneexpressiondataoncellstatetransitionsDEOGEN2http://deogen2.mutaframe.com/PredictionofdeleteriousmutationsinproteinsDNAproDBhttp://dnaprodb.usc.eduStructuralanalysisofDNA鈥損roteincomplexesDSSRhttp://jmol.x3dna.orgDNAandRNAstructurevisualizationDynOmicshttp://dyn.life.nthu.edu.tw/oENM/ProteinmoleculardynamicsusingelasticnetworkmodelsEBISearchhttp://www.ebi.ac.uk/ebisearchWebservicestextsearchinEMBL-EBIdataFireProthttp://loschmidt.chemi.muni.cz/fireprotDesignofthermostableproteinsGalaxyHomomerhttp://galaxy.seoklab.org/cgi-bin/submit.cgi?type=HOMOMERPredictionofproteinhomo-oligomerstructureGASS-WEBhttp://gass.unifei.edu.br/IdentificationofenzymeactivesitesGeMSTONEhttp://gemstone.yulab.org/GeneticvariantprioritizationinhumandiseaseGeneORGANizerhttp://geneorganizer.huji.ac.ilLinkageofhumangenestotheiraffectedbodyorgansGenProBiShttp://genprobis.insilab.orgMappingofSNPstoproteinbindingsitesGEPIAhttp://gepia.cancer-pku.cn/AnalysisofdifferentialgeneexpressionincancerGeSeqhttps://chlorobox.mpimp-golm.mpg.de/geseq.htmlAnnotationofchloroplastgenomesGibbsClusterhttp://www.cbs.dtu.dk/services/GibbsCluster-2.0DetectionofproteinshortlinearmotifsGPCR-SSFE2.0http://www.ssfa-7tmr.de/ssfe2/HomologymodelingofG-proteincoupledreceptorsGWABhttp://www.inetbio.org/gwab/Network-basedgenomewideassociationanalysisHDOCKhttp://hdock.phys.hust.edu.cn/Protein鈥損roteinandprotein鈥揇NA/RNAdockingHGVAhttp://bioinfodev.hpc.cam.ac.uk/web-apps/hgvaArchiveofhumangeneticvariantannotationsHH-MOTiFhttp://chimborazo.biochem.mpg.de/DetectionofproteinshortlinearmotifsI-TASSER-MRhttp://zhanglab.ccmb.med.umich.edu/I-TASSER-MR/ProteinstructuremodelingforX-raycrystallographyINTAAhttp://bioinfo.uochb.cas.cz/INTAA/AnalysisofaminoacidinteractionenergiesIntaRNA2.0http://rna.informatik.uni-freiburg.de/IntaRNA/Input.jspPredictionofinteractionsbetweenRNAmoleculesIslandViewer4.0http://www.pathogenomics.sfu.ca/islandviewer4/Predictionofbacterialgenomicislands(horizontalgenetransfer)kpLogohttp://kplogo.wi.mit.edu/DetectionandvisualizationofshortsequencemotifsLigParGenhttp://jorgensenresearch.com/ligpargenForcefieldparametersformoleculardynamicsLimToxhttp://limtox.bioinfo.cnio.esTextminingforcompoundtoxicitymCSM-NAhttp://structure.bioc.cam.ac.uk/mcsmnaPredictionofproteinmutationeffectonnucleicacidbindingaffinityMicrobiomeAnalysthttp://microbiomeanalyst.caAnalysisofmicrobiomedataMinePathhttp://www.minepath.orgDifferentialexpressionanalysisforregulatorynetworksubpathsModFOLD6http://www.reading.ac.uk/bioinf/ModFOLD/ProteinstructurequalityassessmentmTCTScanhttp://jjwanglab.org/mTCTScanMutationprioritizationforcancerdrugresponseMutaGenehttps://www.ncbi.nlm.nih.gov/projects/mutagene/VisualizationandanalysisofmutationalprofilesincancerNNAlign-2.0http://www.cbs.dtu.dk/services/NNAlign-2.0Detectionofligandmotifsforreceptor鈥搇igandinteractionsNOREVAhttp://server.idrb.cqu.edu.cn/noreva/EvaluationofdatanormalizationmethodsformassspectrometrybasedmetabolomicsdataOlelohttp://www.hpi.de/plattner/oleloTextmininginPubMedDownloadedfromhttps://academic.oup.com/nar/article-abstract/45/W1/W1/3896331/Editorial-the-15th-annual-Nucleic-Acids-ResearchbyShantouUniversityuseron16October2017NucleicAcidsResearch,2017,Vol.45,WebServerissueW3Table1.ContinuedWebServernameURLBriefdescriptionOmicSeqhttp://www.omicseq.orgSearchforomicsdatainmajorrepositoriesP4Phttp://sing.ei.uvigo.es/p4pBacterialstrainclassificationbasedonpeptidedatasetsPathviewhttp://pathview.uncc.edu/VisualizationandannotationofmetabolicpathwayspepATTRACThttp://bioserv.rpbs.univ-paris-diderot.fr/services/pepATTRACTPredictionofprotein鈥損eptidedockingPharmMapperhttp://lilab.ecust.edu.cn/pharmmapperDrugtargetsearchusingpharmacophoremappingPhD-SNPghttp://snps.biofold.org/phd-snpgDeleteriousSNPclassificationPIGSProhttp://cassandra.med.uniroma1.it/AbPrediction/web/pigs.phpModelingofimmunoglobulinvariabledomainsplantiSMASHhttp://plantismash.secondarymetabolites.orgDetectionofbiosyntheticgeneclustersinplantsPMuthttp://mmb.irbbarcelona.org/PMut/PredictionofdiseasepotentialforproteinmutationsPrism3http://prism3.magarveylab.ca/prismPredictionofnaturalproductstructuresfrombiosyntheticgeneclustersProteinsAPIhttp://www.ebi.ac.uk/proteins/apiWebserviceforproteindatafromUniProtKBProteinsPlushttp://proteins.plusStructure-basedmodelingofproteinsProteoSignhttp://bioinformatics.med.uoc.gr/ProteoSignProteindifferentialabundanceanalysisReFOLDhttp://www.reading.ac.uk/bioinf/ReFOLD/ProteinstructurerefinementRegulatorTrailhttps://regulatortrail.bioinf.uni-sb.deAnalysisoftranscriptionfactorsandtargetgenesRiPPMinerhttp://www.nii.ac.in/rippminer.htmlPredictionofchemicalstructuresforribosomallysynthesizedandposttranslationallymodifiedpeptidesRNAworkbenchhttps://github.com/bgruening/galaxy-rna-workbenchStand-alonecollectionoftoolsforanalyzingRNAseqandRNAsequencedataRNA-MoIPhttp://rnamoip.cs.mcgill.ca/PredictionofRNA2Dand3DstructureSBSPKSv2http://www.nii.ac.in/sbspks2.htmlAnalysisofpolyketidesynthasesSCENERYhttp://mensxmachina.org/en/software/NetworkreconstructionfromcytometrydataSDMhttp://structure.bioc.cam.ac.uk/sdm2PredictionofstabilityinproteinmutantsSeMPIhttp://www.pharmaceutical-bioinformatics.de/sempi/PredictionofpolyketidesynthaseproductsfrombiosyntheticgeneclustersSLiMSearchhttp://slim.ucd.ie/slimsearch/DetectionofproteinshortlinearmotifsSODAhttp://protein.bio.unipd.it/soda/PredictionofsolubilityinproteinmutantsSpartaABChttp://spartaabc.tau.ac.il/webserverSequencesimulationwithindelsThreaDomExhttp://zhanglab.ccmb.med.umich.edu/ThreaDomExPredictionofproteindomainsanddomainboundariesToolsatEMBL-EBIhttp://www.ebi.ac.uk/Tools/webservices/WebservicetoolsfromEMBL-EBITraitRateProphttp://traitrate.tau.ac.il/propTestofsequenceevolutionassociationwithphenotypeTRAPPhttp://trapp.h-its.orgAnalysisofproteinbindingsitedynamicsVCF.Filterhttps://biomedical-sequencing.at/VCFFilter/Stand-aloneprogramforfilteringandannotatinggeneticvariantsinvcffilesWeb3DMolhttp://web3dmol.duapp.com/ProteinstructurevisualizationWebGestalthttp://www.webgestalt.org.GenesetfunctionalenrichmentanalysisWoPPERhttp://WoPPER.ba.itb.cnr.it/DetectionofbacterialgenomeregionswithcoordinatedgeneexpressionchangesXSuLThttp://structure.bioc.cam.ac.uk/xsultAnnotationandvisualizationofproteinmultiplesequencealignmentlectionsofwebservices,EBISearchEngine,anupdatefortextsearchintheEMBL-EBIdatarepositories,BioinformaticsToolsfromEMBL-EBI,anupdateonbioinformaticsanalysistools,andProteinsAPI,forproteinassociateddatafromtheUniProtKnowledgebase.Threepapersreportonstand-alonetools,CAFE,foralignment-freecomparisonofgenomesandmetagenomes,VCFFilter,forfilteringandannotatinggeneticvariantsstoredinlargevcffiles,andRNAWorkbench,foranalyzingRNAseqandRNAsequencedata.Inaquesttosupportinnovationinthedevelopmentofstand-alonetools,thisyearI鈥檝eallowedsubmissionsthatareinstalledusingthedockerorcondaenvironments.Theseenvironmentsallowtoolswithmanydependenciestohaveallthesoftwarepartspackagedtogetherinordertosimplifyinstallation.Additionally,theyaidreproducibilitybecauseearlierpackagescanbepreservedevenifthesoftwarepartsthemselvesareupdated.Themajorcomplicationinusingthesepackagesistherequirementofpriorinstallationofsoftwaretohandletheenvironments.Thegoal,noteasilyachieved,isa鈥檕ne-click鈥�installation,anditremainstobeseenifresearcherswillchoosetousethesetypesofresources.Iwelcomefeedbackonthispoint.RNAWorkbench,mentionedabove,isinthiscategory.Goingforward,Iwillcontinuetoevaluatesuchcontainerizedtoolsonacase-by-casebasisandwillbelookingforsignificantaddedvaluebeyondwhatcouldbeobtainedusingacommandlineprogram.Downloadedfromhttps://academic.oup.com/nar/article-abstract/45/W1/W1/3896331/Editorial-the-15th-annual-Nucleic-Acids-ResearchbyShantouUniversityuseron16October2017W4NucleicAcidsResearch,2017,Vol.45,WebServerissueFigure1.Clockwisefromleft:SeanCorbett,DavidJenkinsandTylerFaitsarePhDstudentsintheBostonUniversityBioinformaticsGraduateProgram.JudithMuellerisaresearchscientistwiththeRosettaDesignGroup,whichspecializesinmacromolecularmodeling.TheyprovidedoutstandingassistanceintestingtheWebServerproposalwebsites.Graphicalabstracts.Thisyear,forthefirsttime,theWebServerIssueistryingoutgraphicalabstractsforeachpaper,tobeincludedinthetableofcontents.Agraphicalabstractisavisualrepresentationofthecentralfindingormethodologyofthepaper.Althoughthismaybeachallengeforpapersdescribingwebsitesandcomputationalmethods,therehavebeensomeinterestingsubmissions.Moredetailsontherequirementsforgraphicalabstractsareavailableathttps://academic.oup.com/nar/pages/submissionwebserverandwewillbepostinggoodexamplestouseasguidancefornextyear.Acknowledgements.TheWebServerissuearisesoutoftheworkofmanypeoplewhoIwouldliketothank.First,therearetheresearchersandscientificprogrammerswhoprovideushigh-quality,freelyavailablewebresourcesandwhoreviseandimprovetheirmanuscriptsandwebsitesunderconsiderabletimepressure.Nextarethehundredsofrefereeswhoconscien-tiouslycontributetheirtimetoreviewingandhelpingimprovethemanuscriptsandwebsites.MyownworkismadeenormouslyeasierbythededicatededitorialassistanceofFayOppenheim,whologsthedataforalltheproposalsandinteractswiththereferees,inviting,cajolingandchasingthemsothattheirreviewsarereturnedontime.Thankyou.ThanksalsotoSeanCorbett,TylerFaitsandDavidJenkins,PhDstudentsintheBostonUniversityBioinformaticsProgram,andJudithMueller,aresearchscientistwiththeRosettaDesignGroup,fortheirhardworkincarefullyevaluatingtheproposalwebsitesduringtheproposalapprovalphase(Figure1).AdditionalthankstoMartineBernardes-Silva,EditorialManager,NAR,andJenniferBoydandthestaffatOxfordUniversityPress.Deadlinesfor2018.Tostreamlinethereviewprocess,authorsarerequiredtosendaone-pagesummaryoftheirWebServertotheeditor,DrGaryBenson(narwbsrv@bu.edu),forpre-approvalpriortomanuscriptsubmission.Authorsshouldconsulttheinstructionsforsummarysubmissionandwebsitedesignathttps://academic.oup.com/nar/pages/submissionwebserver.For2018,thesummaryandURLaddressofthefullyfunctionalwebsitemustbesubmittedby31December2017.Thedeadlineforsubmissionofarticlesis31January2018.Instructionsforsubmissions.ReviewofaproposalincludesevaluationofthesummaryandextensivetestingofWebServerfunctionality.Thekeycriteriaforapprovalarehighscientificquality,wideinterest,abilitytodocomputationsonuser-submitteddata,andawell-designed,well-implemented,andfullyfunctionalwebsite.Notethatthereisaminimumtwo-yearDownloadedfromhttps://academic.oup.com/nar/article-abstract/45/W1/W1/3896331/Editorial-the-15th-annual-Nucleic-Acids-ResearchbyShantouUniversityuseron16October2017NucleicAcidsResearch,2017,Vol.45,WebServerissueW5intervalbeforepublicationintheWebServerissueforwebsites,oressentiallysimilarwebsites,thathavebeenthesubjectofapreviouspublication,includinginjournalsotherthanNAR.Withrespecttothewebsite,thefollowingareguidelinesforapproval.1.Itshouldhaveaneasy-to-findsubmissionpagewithasimplemechanismforloadingtestdataandsettingtestparameters.Thepreferredmethodisone-clickloading.Thetestdatashouldbeavailablefordownloadsothatuserscanexaminethedataformat.Additionalmechanismsthatassisttheuserinsubmittingdatashouldbeimplementedwhereappropriate,forexample,automaticloadingofapdbstructurefileoncetheuserhasenteredtheappropriateidentifier.2.Outputshouldbedynamicandrichindetail.Whereverpossible,supportingevidenceusedincalculationsand/orlinkstoexternaldatabasescontainingadditionalinformationshouldbeprovided.Numerical,textualandgraphicaloutputshouldbemixedandvisualizationtoolsthataddinformationorincreasetheuser鈥檚understandingshouldbeutilized.Notethatoutputconsistingmerelyofafewnumericalvalues,astaticspreadsheet,oraseriesoffilestobeopenedinotherprogramswillnotbeapproved.Notealsothatforsecurityreasons,useofFLASHandJavapluginswillnolongerbeallowed.3.Webserversthatdonotfinishtheircalculationsimmediatelymustimplementamechanismforreturningresultstotheuser.Notificationbyemailmaybeprovidedasanoption,butanalternativethatreturnsaweblinkatthetimeofdatasubmission,whichtheusercanthenbookmarkandaccessatalatertime,isrequired.Thislinkshouldideallyreportthestatusofthejob(queued,running,finished)andanestimateoftheoveralltimeforjobcompletion.Websitesthatrequireaguestloginwillnotbeapproved.Notethatuploadeddataandtheresultsofanalysisforeachusermustbeprivateandnotviewablebyotherusers.4.Thewebsiteshouldbesupportedbyanextensivehelpsectionortutorialthatguidestheuserthroughthesubmissionprocess,containsdetailsaboutinputfileformatsandparameters,andexplainsthemeaningoftheoutput.Wheneverpossible,thehelppagesshouldlinktodynamicoutputexamplessimilartothoseprovidedbythewebsite.Whenvideotutorialsareused,textandfigurehelppagesshouldalsobeavailabletosimplifyquicklook-up.5.AnyproposalforaWebServerthatispredictivemustincludedetailsonvalidationofpredictionsfromnewdatanotusedintraining.N-foldcrossvalidationmethodswillnotbeconsideredsufficient.Detailsshouldincludesizeandcompositionofthevalidationdataset(numberofpositiveandnegativecases),andseveralmeasuresofpredictiveperformance,in-cludingsensitivity,specificityandprecision.Proposalsarefrequentlyrejectedforlackofadequatepredictionvalidationinformation.6.Websitesnotclearlydesignedtoacceptandanalyzeuser-submitteddatawillberejected.Thisappliestothoseestablishedprimarilyforlookuporexplorationinadataset,orservethefunctionof鈥榙ataaggregators.鈥�AuthorsofwebsitesthatprovidenoveldatashouldconsidertheNARDatabaseIssueasapossiblevenue(seetheinstructionsathttps://academic.oup.com/nar/pages/msprepdatabase).7.ProposalsthatdescribeanewanalysismethodaregenerallynotappropriatefortheWebServerissuebecauselimitedspaceandtherapidrevisionprocessmakethoroughmethoddescriptionandvalidationproblematic.AuthorsofsuchmethodsmightinsteadconsidersendingtheirmanuscripttoNARasaregularcomputationalbiologypaper(seetheinstructionsforauthorsathttps://academic.oup.com/nar/pages/CriteriaScope#Computational%20Biology).GaryBensonExecutiveEditorWebServerIssueNucleicAcidsResearchDownloadedfromhttps:/