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NucleicAcidsResearch2010DatabaseIssue,ACLAME:ACLAssificationofMobilegeneticElements,update2010,TheACLAMEdatabaseisdedicatedtothecollection,analysisandclassificationofsequencedmobilegeneticelements(MGEs,inparticularphagesandplasmids).InadditiontoprovidinginformationontheMGEscontent,classificationsareavailableatvariouslevelsoforganization.Atthegene/proteinlevel,familiesgroupsimilarsequencesthatareexpectedtosharethesamefunction.FamiliesoffourormoreproteinsaremanuallyassignedwithafunctionalannotationusingtheGeneOntologyandthelocallydevelopedontologyMeGOdedicatedtoMGEs.Atthegenomelevel,evolutionarycohesivemodulesgroupsetsofproteinfamiliessharedamongMGEs.Atthepopulationlevel,networksdisplaythereticulateevolutionaryrelationshipsamongMGEs.Toincreasethecoverageofthephagesequencespace,ACLAMEversion0.4incorporates760high-qualitypredictedprophagesselectedfromtheProphinderdatabase.MostofthedatacanbedownloadedfromthefreelyaccessibleACLAMEwebsite(http:/aclame.ulb.ac.be).TheBLASTinterfaceforqueryingthedatabasehasbeenextendedandnumeroustoolsforin-depthanalysisoftheresultshavebeenadded.,ISbrowser:anextensionofISfinderforvisualizinginsertionsequencesinprokaryoticgenomes,Insertionsequences(ISs)areamongthesmallestandsimplestautonomoustransposableelements.ISfinder(http:/www-is.biotoul.fr/)isadedicatedISdatabasewhichassignsnamestoindividualISstomaintainacoherentnomenclature,anISrepositoryincluding3000individualISsfrombothbacteriaandarchaeaandprovidesabasisforISclassification.EachISisindexedinISfinderwithvariousassociatedpiecesofinformation(thecompletenucleotidesequence,thesequenceoftheendsandtargetsites,potentialopenreadingframes,strainoforigin,distributioninotherstrainsandavailablebibliography)andclassifiedintoagrouporfamilytoprovidesomeinsightintoitsphylogeny.ISfinderalsoincludesextensivebackgroundinformationonISsandtransposonsingeneral.Onlinetoolsaregraduallybeingadded.Atpresent,itisdifficulttovisualizetheglobaldistributionofISsinagivenbacterialgenome.Suchinformationwouldfacilitateunderstandingoftheimpactofthesesmalltransposableelementsonshapingtheirhostgenome.HerewedescribeISbrowser(http:/www-genome.biotoul.fr/ISbrowser.php),anextensiontotheISfinderplatformandatoolwhichpermitsvisualizationoftheposition,orientationanddistributionofcompleteandpartialISsinindividualprokaryoticgenomes.,RegPrecise:adatabaseofcuratedgenomicinferencesoftranscriptionalregulatoryinteractionsinprokaryotes,TheRegPrecisedatabase()wasdevelopedforcapturing,visualizationandanalysisofpredictedtranscriptionfactorregulonsinprokaryotesthatwerereconstructedandmanuallycuratedbyutilizingthecomparativegenomicapproach.Asignificantnumberofhigh-qualityinferencesoftranscriptionalregulatoryinteractionshavebeenalreadyaccumulatedfordiversetaxonomicgroupsofbacteria.Thereconstructedregulonsincludetranscriptionfactors,theircognateDNAmotifsandregulatedgenes/operonslinkedtothecandidatetranscriptionfactorbindingsites.TheRegPreciseallowsforbrowsingthereguloncollectionsfor:(i)conservationofDNAbindingsitesandregulatedgenesforaparticularregulonacrossdiversetaxonomiclineages;(ii)setsofregulonsforafamilyoftranscriptionfactors;(iii)repertoireofregulonsinaparticulartaxonomicgroupofspecies;(iv)regulonsassociatedwithametabolicpathwayorabiologicalprocessinvariousgenomes.Theinitialreleaseofthedatabaseincludes11500candidatebindingsitesfor400orthologousgroupsoftranscriptionfactorsfromover350prokaryoticgenomes.Majorityofthesedataarerepresentedbygenome-wideregulonreconstructionsinShewanellaandStreptococcusgeneraandalarge-scalepredictionofregulonsfortheLacIfamilyoftranscriptionfactors.Anothersectioninthedatabaserepresentstheresultsofaccurateregulonpropagationtothecloselyrelatedgenomes.,PROSITE,aproteindomaindatabaseforfunctionalcharacterizationandannotation,PROSITEconsistsofdocumentationentriesdescribingproteindomains,familiesandfunctionalsites,aswellasassociatedpatternsandprofilestoidentifythem.ItiscomplementedbyProRule,acollectionofrulesbasedonprofilesandpatterns,whichincreasesthediscriminatorypoweroftheseprofilesandpatternsbyprovidingadditionalinformationaboutfunctionallyand/orstructurallycriticalaminoacids.PROSITEislargelyusedfortheannotationofdomainfeaturesofUniProtKB/Swiss-Protentries.Amongthe983(DNA-binding)domains,repeatsandzincfingerspresentinSwiss-Prot(release57.8of22September2009),696(70%)areannotatedwithPROSITEdescriptorsusinginformationfromProRule.Inordertoallowbetterfunctionalcharacterizationofdomains,PROSITEdevelopmentsfocusonsubfamilyspecificprofilesandanewprofilebuildingmethodgivingmoreweighttofunctionallyimportantresidues.Here,wedescribeAMSA,anannotatedmultiplesequencealignmentformatusedtobuildanewgenerationofgeneralizedprofiles,themigrationofScanPrositetoVital-IT,aclusterof633CPUs,andtheadoptionoftheDistributedAnnotationSystem(DAS)tofacilitatePROSITEdataintegrationandinterchangewithothersources.ThelatestversionofPROSITE(release20.54,of22September2009)contains1308patterns,863profilesand869ProRules.PROSITEisaccessibleat:/prosite/.,PANTHERversion7:improvedphylogenetictrees,orthologsandcollaborationwiththeGeneOntologyConsortium,ProteinAnalysisTHroughEvolutionaryRelationships(PANTHER)isacomprehensivesoftwaresystemforinferringthefunctionsofgenesbasedontheirevolutionaryrelationships.PhylogenetictreesofgenefamiliesformthebasisforPANTHERandthesetreesareannotatedwithontologytermsdescribingtheevolutionofgenefunctionfromancestraltomoderndaygenes.OneofthemainapplicationsofPANTHERisinaccuratepredictionofthefunctionsofuncharacterizedgenes,basedontheirevolutionaryrelationshipstogeneswithfunctionsknownfromexperiment.ThePANTHERwebsite,freelyavailableat,alsoincludessoftwaretoolsforanalyzinggenomicdatarelativetoknownandinferredgenefunctions.Since2007,therehavebeenseveralnewdevelopmentstoPANTHER:(i)improvedphylogenetictrees,explicitlyrepresentingspeciationandgeneduplicationevents,(ii)identificationofgeneorthologs,includingleastdivergedorthologs(bestone-to-onepairs),(iii)coverageofmoregenomes(48genomes,upto87%ofgenesineachgenome;see/panther/summaryStats.jsp),(iv)improvedsupportforalternativedatabaseidentifiersforgenes,proteinsandmicroarrayprobesand(v)adoptionoftheSBGNstandardfordisplayofbiologicalpathways.Inaddition,PANTHERtreesarebeingannotatedwithgenefunctionaspartoftheGeneOntologyReferenceGenomeproject,resultinginanincreasingnumberofcuratedfunctionalannotations.,MEROPS:thepeptidasedatabase,Peptidases,theirsubstratesandinhibitorsareofgreatrelevancetobiology,medicineandbiotechnology.TheMEROPSdatabase(http:/merops.sanger.ac.uk)aimstofulfiltheneedforanintegratedsourceofinformationaboutthese.Thedatabasehasahierarchicalclassificationinwhichhomologoussetsofpeptidasesandproteininhibitorsaregroupedintoproteinspecies,whicharegroupedintofamilies,whichareinturngroupedintoclans.Theclassificationframeworkisusedforattachinginformationateachlevel.Animportantfocusofthedatabasehasbecomedistinguishingonepeptidasefromanotherthroughidentifyingthespecificityofthepeptidaseintermsofwhereitwillcleavesubstratesandwithwhichinhibitorsitwillinteract.Wehavecollectedover39000knowncleavagesitesinproteins,peptidesandsyntheticsubstrates.Theseallowustodisplaypeptidasespecificityandalignmentsofproteinsubstratestogiveanindicationofhowwellacleavagesiteisconserved,andthusitsprobablephysiologicalrelevance.Whilethenumberofnewpeptidasefamiliesandclanshasonlygrownslowlythenumberofcompletegenomeshasgreatlyincreased.Thishasallowedustoaddananalysistooltotherelevantspeciespagestoshowsignificantgainsandlossesofpeptidasegenesrelativetorelatedspecies.,Thecomprehensivemicrobialresource,TheComprehensiveMicrobialResourceorCMR()providesaweb-basedcentralresourceforthedisplay,searchandanalysisofthesequenceandannotationforcompleteandpubliclyavailablebacterialandarchaealgenomes.InadditiontodisplayingtheoriginalannotationfromGenBank,theCMRmakesavailablesecondaryautomatedstructuralandfunctionalannotationacrossallgenomestoprovideconsistentdatatypesnecessaryforeffectiveminingofgenomicdata.Precomputedhomologysearchesarestoredtoallowmeaningfulgenomecomparisons.TheCMRsuppliesuserswithover50differenttoolstoutilizethesequenceandannotationdataacrossoneormoreofthe571currentlyavailablegenomes.Atthegeneleveluserscanviewthegeneannotationandunderlyingevidence.Genomelevelinformationincludeswholegenomegraphicaldisplays,biochemicalpathwaymapsandgenomesummarydata.Comparativetoolsdisplayanalysisbetweengenomeswithhomologyandgenomealignmenttools,andsearchesacrosstheaccessions,annotation,andevidenceassignedtoallgenes/genomesareavailable.ThedataandtoolsontheCMRaidgenomicresearchandanalysis,andtheCMRisincludedinover200scientificpublications.ThecodeunderlyingtheCMRwebsiteandtheCMRdatabasearefreelyavailablefordownloadwithnolicenserestrictions.,MBGDupdate2010:towardacomprehensiveresourceforexploringmicrobialgenomediversity,Themicrobialgenomedatabase(MBGD)forcomparativeanalysisisaplatformformicrobialcomparativegenomicsbasedonautomatedorthologgroupidentification.AprominentfeatureofMBGDisthatitallowsuserstocreateorthologgroupsusingaspecifiedsubgroupoforganisms.Thedatabaseisconstantlyupdatedandnowcontainsalmost1000genomes.ToutilizetheMBGDdatabaseasacomprehensiveresourceforinvestigatingmicrobialgenomediversity,wehavedevelopedthefollowingadvancedfunctionalities:(i)enhancedassignmentoffunctionalannotation,includingexternaldatabaselinkstoeachorthologousgroup,(ii)interfaceforchoosingasetofgenomestocomparebasedonphenotypicproperties,(iii)theadditionofmoreeukaryoticmicrobialgenomes(fungiandprotists)andsomehighereukaryotesasreferencesand(iv)enhancementoftheMyMBGDmode,whichallowsuserstoaddtheirowngenomestoMBGDandnowacceptsrawgenomicsequenceswithoutanyannotation(insuchacase,itrunsagene-findingprocedurebeforeidentifyingtheorthologs).Someanalysisfunctions,suchasthefunctiontofindorthologswithsimilarphylogeneticpatterns,havealsobeenimproved.MBGDisaccessibleathttp:/mbgd.genome.ad.jp/.,phiSITE:databaseofgeneregulationinbacteriophages,WehavedevelopedphiSITE,databaseofgeneregulationinbacteriophages.Todateitcontainsdetailedinformationaboutmorethan700experimentallyconfirmedorpredictedregulatoryelements(promoters,operators,terminatorsandattachmentsites)from32bacteriophagesbelongingtoSiphoviridae,MyoviridaeandPodoviridaefamilies.Thedatabaseismanuallycurated,thedataarecollectedmainlyformscientificpapers,cross-referencedwithotherdatabaseresources(EMBL,UniProt,NCBItaxonomydatabase,NCBIGenome,ICTVdb,PubMedCentral)andstoredinSQLbaseddatabasesystem.Thesystemprovidesfulltextsearchforregulatoryelements,graphicalvisualizationofphagegenomesandseveralexportoptions.Inaddition,visualizationsofgeneregulatorynetworksforfivephages(BacillusphageGA-1,Enterobacteriaphagelambda,EnterobacteriaphageMu,EnterobacteriaphageP2andMycoplasmaphageP1)havebeendefinedandmadeavailable.ThephiSITEisaccessibleat/.,Theintegratedmicrobialgenomessystem:anexpandingcomparativeanalysisresource,Theintegratedmicrobialgenomes(IMG)systemservesasacommunityresourceforcomparativeanalysisofpubliclyavailablegenomesinacomprehensiveintegratedcontext.IMGcontainsbothdraftandcompletemicrobialgenomesintegratedwithotherpubliclyavailablegenomesfromallthreedomainsoflife,togetherwithalargenumberofplasmidsandviruses.IMGprovidestoolsandviewersforanalyzingandreviewingtheannotationsofgenesandgenomesinacomparativecontext.Sinceitsfirstreleasein2005,IMGsdatacontentandanalyticalcapabilitieshavebeenconstantlyexpandedthroughregularreleases.SeveralcompanionIMGsystemshavebeensetupinordertoservedomainspecificneeds,suchasexpertreviewofgenomeannotations.IMGisavailableat.,MicrobesOnline:anintegratedportalforcomparativeandfunctionalgenomics,Since2003,MicrobesOnline()hasbeenprovidingacommunityresourceforcomparativeandfunctionalgenomeanalysis.Theportalincludesover1000completegenomesofbacteria,archaeaandfungiandthousandsofexpressionmicroarraysfromdiverseorganismsrangingfrommodelorganismssuchasEscherichiacoliandSaccharomycescerevisiaetoenvironmentalmicrobessuchasDesulfovibriovulgarisandShewanellaoneidensis.Toassistinannotatinggenesandinreconstructingtheirevolutionaryhistory,MicrobesOnlineincludesacomparativegenomebrowserbasedonphylogenetictreesforeverygenefamilyaswellasaspeciestree.Toidentifyco-regulatedgenes,MicrobesOnlinecansearchforgenesbasedontheirexpressionprofile,andprovidestoolsforidentifyingregulatorymotifsandseeingiftheyareconserved.MicrobesOnlinealsoincludesfastphylogeneticprofilesearches,comparativeviewsofmetabolicpathways,operonpredictions,aworkbenchforsequenceanalysisandintegrationwithRegTransBaseandothermicrobialgenomeresources.ThenextupdateofMicrobesOnlinewillcontainsignificantnewfunctionality,includingcomparativeanalysisofmetagenomicsequencedata.Programmaticaccesstothedatabase,alongwithsourcecodeanddocumentation,isavailableat/programmers.html.,TheMiST2database:acomprehensivegenomicsresourceonmicrobialsignaltransduction,TheMiST2database()identifiesandcatalogstherepertoireofsignaltransductionproteinsinmicrobialgenomes.Signaltransductionsystemsregulatethemajorityofcellularactivitiesincludingthemetabolism,development,host-recognition,biofilmproduction,virulence,andantibioticresistanceofhumanpathogens.Thus,knowledgeoftheproteinsandinteractionsthatcomprisethesecommunicationnetworksisanessentialcomponenttofurtheringbiomedicaldiscovery.Theseareidentifiedbysearchingproteinsequencesforspecificdomainprofilesthatimplicateaproteininsignaltransduction.Comparedtothepreviousversionofthedatabase,MiST2containsahostofnewfeaturesandimprovementsincludingthefollowing:draftgenomes;extracytoplasmicfunction(ECF)sigmafactorproteinidentification;enhancedclassificationofsignalingproteins;novel,high-qualitydomainmodelsforidentifyinghistidinekinasesandresponseregulators;neighboringtwo-componentgenes;genecart;bettersearchcapabilities;enhancedtaxonomybrowser;advancedgenomebrowser;andamodern,biologist-friendlywebinterface.MiST2currentlycontains966completeand157draftbacterialandarchaealgenomes,whichcollectivelycontainmorethan245000signaltransductionproteins.Themajority(66%)oftheseareone-componentsystems,followedbytwo-componentproteins(26%),chemotaxis(6%),andfinallyECFfactors(2%).,TheUCSCGenomeBrowserdatabase:update2010,TheUniversityofCalifornia,SantaCruz(UCSC)GenomeBrowserwebsite(/)providesalargedatabaseofpubliclyavailablesequenceandannotationdataalongwithanintegratedtoolsetforexaminingandcomparingthegenomesoforganisms,aligningsequencetogenomes,anddisplayingandsharingusersownannotationdata.AsofSeptember2009,genomicsequenceandabasicsetofannotationtracksareprovidedfor47organisms,including14mammals,10non-mammalvertebrates,3invertebratedeuterostomes,13insects,6wormsandayeast.Newdatahighlightsthisyearincludeanupdatedhumangenomebrowser,a44-speciesmultiplesequencealignmenttrack,improvedvariationandphenotypetracksand16newgenome-wideENCODEtracks.Newfeaturesincludedrag-and-zoomnavigation,aWikitrackforuser-addedannotations,newcustomtrackformatsforlargedatasets(bigBedandbigWig),anewmultiplealignmentoutputtool,linkstovariationandproteinstructuretools,insilicoPCRutilityenhancements,andimprovedtrackconfigurationtools.,TheProteomicsIdentificationsdatabase:2010update,TheProteomicsIdentificationsdatabase(PRIDE,http:/www.ebi.ac.uk/pride)attheEuropeanBioinformaticsInstitutehasbecomeoneofthemainrepositoriesofmassspectrometry-derivedproteomicsdata.Forthelast2years,PRIDEdataholdingshavegrownsubstantially,comprising60differentspecies,morethan2.5millionproteinidentifications,11.5millionpeptidesandover50millionspectrabySeptember2009.WeheredescribeseveralnewandimprovedfeaturesinPRIDE,includingtherevisedsubmissionprocess,whichnowincludesdirectsubmissionoffragmentionannotations.Correspondingly,itisnowpossibletovisualizespectrumfragmentationannotationsontandemmassspectra,akeyfeatureforcompliancewithjournaldatasubmissionrequirements.WealsodescriberecentdevelopmentsinthePRIDEBioMartinterface,whichnowallowsintegrativequeriesthatcanjoinPRIDEdatatoagrowingnumberofbiologicalresourcessuchasReactome,Ensembl,InterProandUniProt.Thisabilitytoperformextremelypowerfulacross-domainquerieswillcertainlybeacornerstoneoffuturebioinformaticsanalyses.Finally,wehighlighttheimportanceofdatasharingintheproteomicsfield,andthecorrespondingintegrationofPRIDEwithotherdatabasesintheProteomExchangeconsortium.,CAMP:ausefulresourceforresearchonantimicrobialpeptides,Antimicrobialpeptides(AMPs)aregainingpopularityasbettersubstitutetoantibiotics.Thesepeptidesareshowntobeactiveagainstseveralbacteria,fungi,viruses,protozoaandcancerouscells.UnderstandingtheroleofprimarystructureofAMPsintheirspecificityandactivityisessentialfortheirrationaldesignasdrugs.CollectionofAnti-MicrobialPeptides(CAMP)isafreeonlinedatabasethathasbeendevelopedforadvancementofthepresentunderstandingonantimicrobialpeptides.Itismanuallycuratedandcurrentlyholds3782antimicrobialsequences.Thesesequencesaredividedintoexperimentallyvalidated(patentsandnon-patents:2766)andpredicted(1016)datasetsbasedontheirreferenceliterature.Informationlikesourceorganism,activity(MICvalues),referenceliterature,targetandnon-targetorganismsofAMPsarecapturedinthedatabase.Theexperimentallyvalidateddat
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