简介：Circulargenomes,beingthelargestproportionofsequencedgenomes,playanimportantroleingenomeanalysis.However,traditional2Dcircularmaponlyprovidesanoverviewandannotationsofgenomebutdoesnotofferfeature-basedcomparison.Forremedyingtheseshortcomings,wedeveloped3DGenomeTuner,ahybridofcircularmapandcomparativemaptools.Itscapabilityofviewingcomparisonsbetweenmultiplecircularmapsina3Dspaceoffersgreatbenefitstothestudyofcomparativegenomics.Theprogramisfreelyavailable(underanLGPLlicence)athttp://sourceforge.net/projects/dgenometuner.

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简介：InordertodevelopclinicaldiagnostictoolsforrapiddetectionofSARS-CoV(severeacuterespiratorysyndrome-associatedcoronavirus)andtoidentifycandidateproteinsforvaccinedevelopment,theC-terminalportionofthenucleocapsid(NC)genewasamplifiedusingRT-PCRfromtheSARS-CoVgenome,clonedintoayeastexpressionvector(pEGH),andexpressedasaglutathioneS-transferase(GST)andHisx6double-taggedfusionproteinunderthecontrolofaninduciblepromoter.WesternanalysisonthepurifiedproteinconfirmedtheexpressionandpurificationoftheNCfusionproteinsfromyeast.Todetermineitsantigenicity,thefusionproteinwaschallengedwithserumsamplesfromSARSpatientsandnormalcontrols.TheNCfusionproteindemonstratedhighantigenicitywithhighspecificity,andtherefore,itshouldhavegreatpotentialindesigningclinicaldiagnostictoolsandprovideusefulinformationforvaccinedevelopment.

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简介：Ithasbeenshownthattheprogressinthedeterminationofmembraneproteinstructuregrowsexponentially,withapproximatelythesamegrowthrateasthatofthewater-solubleproteins.Inordertoinvestigatetheeffectofthis,ontheperformanceofpredictionalgorithmsforbothα-helicalandβ-barrelmembraneproteins,weconductedaprospectivestudybasedonhistoricalrecords.WetrainedseparatehiddenMarkovmodelswithdifferentsizedtrainingsetsandevaluatedtheirperformanceontopologypredictionforthetwoclassesoftransmembraneproteins.Weshowthattheexistingtop-scoringalgorithmsforpredictingthetransmembranesegmentsofα-helicalmembraneproteinsperformslightlybetterthanthatofβ-barreloutermembraneproteinsinallmeasuresofaccuracy.Withthesamerationale,ameta-analysisoftheperformanceofthesecondarystructurepredictionalgorithmsindicatesthatexistingalgorithmictechniquescannotbefurtherimprovedbyjustaddingmorenon-homologoussequencestothetrainingsets.Theupperlimitforsecondarystructurepredictionisestimatedtobenomorethan70%and80%ofcorrectlypredictedresiduesforsinglesequencebasedmethodsandmultiplesequencebasedones,respectively.Therefore,weshouldconcentrateoureffortsonutilizingnewtechniquesforthedevelopmentofevenbetterscoringpredictors.

简介：Leishmaniaisassociatedwithabroadspectrumofdiseases,rangingfromsimplecutaneoustoinvasivevisceralleishmaniasis.Here,thesequencesoftencysteineproteasesoftypesA,BandCofLeishmaniamajorwereobtainedfromGeneDBdatabase.PredictionofMHCclassIepitopesofthesecysteineproteaseswasperformedbyNetCTLprogramversion1.2.Inaddition,byusingBcePredserver,differentstructuralpropertiesoftheproteinswerepredictedtofindouttheirpotentialBcellepitopes.Accordingtothiscomputationalanalysis,nineregionswerepredictedasBcellepitopes.Theresultsprovideusefulinformationfordesigningpeptide-basedvaccines.

简介：在染色体为特定的DNA目标设计锌手指蛋白质主题在染色体工程的领域里是批评的。我们为为绑在特定的目标DNA地点的C2H2锌手指预言识别helices开发了一个计算方法。这预言用锌手指蛋白质和他们的目标DNA三位字节的彻底的数据集基于人工的神经网络。用户们能为也要预言在的二或三根锌手指选择选择一模块化或为输入DNA顺序的synergistic时尚。这个方法将为对为几个生物、生物医学的应用程序设计特定的锌手指抄写因素和锌手指核酸酶感兴趣的研究人员是珍贵的。网工具ZiF预言在http://web.iitd.ac.in/sundar/zifpredict/在网上是可得到的。

简介：Werecentlyreportedtheuseofagene-trappingapproachtoisolatecellclonesinwhichareportergenehadintegratedintogenesmodulatedbyT-cellactivation.WehavenowtestedapanelofclonesfromthatreportandidentifiedtheonethatrespondstoavarietyofG-proteincoupledreceptors(GPCR).TheβlactamasetaggedEGR-3JurkatcellwasusedtodissectspecificGPCRsignalinginvivo.ThreeGPCRswerestudied,includingthechemokinereceptorCXCR4(Gicoupled)thatwasendogenouslyexpressed,theplateletactivationfactor(PAF)receptor(Gq-coupled),andβ2adrenergicreceptor(Gs-coupled)thatwasbothstablytransfected.Agonistsforeachreceptoractivatedtranscriptionoftheβ-lactamasetaggedEGR-3gene.InductionofEGR-3throughCXCR4wasblockedbypertussistoxinandPD58059,aspecificinhibitorofMEK(MAPK/ERKkinase).NeitheroftheseinhibitorsblockedisoproterenolorPAF-mediatedactivationofEGR-3.Conversely,β2-andPAF-mediatedEGR-3activationwasblockedbythep38,specificinhibitorSB580.Inaddition,bothβ2-andPAF-mediatedEGR-3activationcouldbesynergisticallyactivatedbyCXCR4activation.ThiscombinedresultindicatesthatEGR-3canbeactivatedthroughdistinctsignaltransductionpathwaysbydifferentGPCRsandthatsignalscanbeintegratedandamplifiedtoefficientlytunethelevelofactivation.