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

简介：TheNetAcetmethodhasbeendevelopedtomakepredictionsofN-terminalacetylationsites,butmoreinformationofthedatasetcouldbeutilizedtoimprovetheperformanceofthemodel.Byemployinganewwaytoextractpatternsfromsequencesandusingasamplebalancingmechanism,weobtainedacorrelationcoefficientof0.85,andasensitivityof93%onanindependentmammaliandataset.Awebserverutilizingthismethodhasbeenconstructedandisavailableathttp://166.111.24.5/acetylation.html.

简介：流行性感冒A病毒(H1N1)2009，一个新猪起源流行性感冒A病毒，世界范围地被散布了并且引起了大公共害怕。高产量的transcriptomics和proteomics方法现在正在被使用识别H1N1和H1N1主人相互作用。这篇文章在H1N1诊断，处理，和H1N1病毒主人相互作用考察最近的transcriptomics和proteomics研究，到为进一步理解感染机制并且控制H1N1传播提供一些帮助。

简介：TheCoronaviridaefamilyischaracterizedbyanucleocapsidthatiscomposedofthegenomeRNAmoleculeincombinationwiththenucleoprotein(Nprotein)withinavirion.ThemoststrikingphysiochemicalfeatureoftheNproteinofSARS-CoVisthatitisatypicalbasicproteinwithahighpredictedpIandhighhydrophilicity,whichisconsistentwithitsfunctionofbindingtotheribophosphatebackboneoftheRNAmolecule.ThepredictedhighextentofphosphorylationoftheNproteinonmultiplecandidatephosphorylationsitesdemonstratesthatitwouldberelatedtoimportantfunctions,suchasRNA-bindingandlocalizationtothenucleolusofhostcells.SubsequentstudyshowsthatthereisanSR-richregionintheNproteinandthisregionmightbeinvolvedintheprotein-proteininteraction.TheabundantantigenicsitespredictedintheNprotein,aswellasexperimentalevidencewithsynthesizedpolypeptides,indicatethattheNproteinisoneofthemajorantigensoftheSARS-CoV.Comparedwithotherviralstructuralproteins,thelowvariationrateoftheNproteinwithregardstoitssizesuggestsitsimportancetothesurvivalofthevirus.

简介：Thesurfaceglycoproteinhemagglutinin(HA)helpstheinfluenzaAvirustoevadethehostimmunesystembyantigenicvariationandisamajordrivingforceforviralevolution.Inthisstudy,theselectionpressureonHAofH5N1influenzaAviruswasanalyzedusingbioinformaticsalgorithms.Mostoftheidentifiedpositiveselection(PS)siteswerefoundtobewithinoradjacenttoepitopesites.SomeoftheidentifiedPSsitesareconsistentwithpreviousexperimentalstudies,providingfurthersupporttothebiologicalsignificanceofourfindings.ThehighestfrequencyofPSsiteswasobservedinrecentstrainsisolatedduring2005–2007.PhylogeneticanalysiswasalsoconductedonHAsequencesfromvarioushosts.Viraldriftisalmostsimilarinbothavianandhumanspecieswithaprogressivetrendovertheyears.OurstudyreportsnewmutationsinfunctionalregionsofHAthatmightprovidemarkersforvaccinedesignorcanbeusedtopredictisolatesofpandemicpotential.

简介：预言潜水艇的能力从它的顺序的蛋白质的细胞的本地化是很重要的，它关于蛋白质的功能提供信息。我们在场一个计算工具，PredSL，它利用神经网络，Markov链，隐藏的Markov建模的侧面，和得分为潜水艇的预言的矩阵在从N终端氨基酸顺序的真核细胞的房间的蛋白质的细胞的本地化。它试图分类蛋白质进五个组：叶绿体，thylakoid，线粒体，能分泌的小径，和“其它”。当在一个五倍的交叉验证过程测试了时，PredSL分别地为植物和非植物数据集表明86.7%和87.1%全面精确性。与TargetP，迄今为止是最广泛地使用的方法，和LumenP相比，PredSL的结果在大多数情况中是可比较的。当在Saccharomycescerevisiae染色体的试验性地验证的蛋白质上测试了时，PredSL可比较地表现如果比为一样的任务的任何可得到的算法不好。而且，PredSL是为这些的预言有能力的唯一的方法代替作为通过URL:http://bioinformatics.biol.uoa.gr/PredSL/的独立应用可得到的细胞的本地化。

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：细螺旋体病是螺旋体种类引起的传染细菌的疾病。在这研究，我们克隆并且定序从L编码immunodominant蛋白质GroEL的基因。interrogansserovarAutumnalis种类N2，在Chennai在细螺旋体病的爆发期间从一个病人的尿被孤立，印度。这groEL基因另外的leptospiralserovars与相同(99%类似)的高度编码60kDa的蛋白质到那些。RecombinantGroEL是在Escherichiacoli的overexpressed。当没有反应从seronegative控制病人与sera被观察时，Immunoblot分析显示从证实的细螺旋体病病人的sera与recombinantGroEL显示出强壮的反应。另外，GroEL的3D结构作为模板从Thermusthermophilus用chaperonin建筑群cpn60被构造并且验证。结果显示了8.35的Z分数，它在对为蛋白质的期望的价值的好同意。cpn60结构的Ca踪迹和leptospiralGroEL的预言的结构的重叠与1.5的RMSD价值显示第二等的结构元素的好同意?。进一步的学习是必要的作为一个疫苗的部件为细螺旋体病的血清学的诊断并且为它的潜力评估GroEL。

简介：以便获得米饭幼仔圆锥花序proteome的高分辨率的electrophorogram，我们评估了通常使用在的各种各样的协议二维(2D)蛋白质的polyacrylamide胶化电气泳动(页)包括染色协议的胶化，使不能调动的pH坡度(IPG)的pH范围脱衣并且样品装载数量。结果证明染色协议使用的银敏化包含冰川的醋酸，钠醋酸盐和钠thiosulfate的答案(在1988由Heukeshoven和Dernick报导了)并且染色方法使用答案包含的Coomassie灿烂的蓝色G-250，铵硫酸盐和磷的酸(在2010由粉红色的等报导了)表明了优异染色效果。另外，当有5-8的pH范围的IPG胶化长带被使用时，我们也与4-7的pH范围证明更高的分辨率被完成，与那相比。最后，最佳的装载数量作为与染色协议的银硝酸盐在联合与pH5-8使用17厘米长的非线性的IPG长带的130g被决定。评估结果将在年轻米饭颖果的proteome分析是有用的。

简介：流行性感冒A病毒(H1N1)，人的地方性的紧张的一个基因分类，鸟并且猪流感，穿过种类障碍到人并且显然获得了人的能力到人的传播。因为NS1蛋白质禁止抗病毒的干扰素/生产，H5N1子类型的一些紧张是高度剧毒的。另一蛋白质NS2调停到通过出口的细胞质的从原子核的病毒的ribonucleoprotein的出口信号。在这份报纸，我们学习了H1N1子类型的这些蛋白质的结构功能关系并且决定了他们的致病力的原因。我们的结果证明非保守的变化稍微稳定了或使动摇NS1或NS1-dsRNA建筑群的结构的域，稍微因此增加了或减少NS1蛋白质并且因而的函数提高了或减少H1N1病毒的致病力。不同紧张的NS2蛋白质在不同领域带了非保守的变化，导致功能的细微损失。这些变化稍微减少了病毒的致病力。因此，结果证实这些病毒的蛋白质的结构功能关系。

简介：InFebruary2006,twooutbreaksofhighlypathogenicavianinfluenzaAvirussubtypeH5N1occurredinchickensintwoneighboringdistricts(firstinNandurbarandsecondinJalgaon)ofMaharashtra,India,inaspanof12days.Inthepresentstudy,theneuraminidase(NA)geneofthetwoIndianH5N1isolateswastakenintoconsiderationtofindifthetwostrainsaregeneticallysimilar.PhylogeneticanalysisoftheNAgeneshowedthattheH5N1strainsisolatedfromthetwooutbreakswerenotoriginatedfromthesamesource.ThefirstIndianisolate(Nandubar/7972/06)wasclusteredclosesttoanisolatefromchickeninVietnamin2004,whereasthesecondIndianisolate(Jalgaon/8824/06)showedresemblancetostrainsisolatedfromswaninItalyandIranin2006.Moreover,aminoacidsequenceanalysisshowedvaryinghotspotsforsubstitutionsbetweenthesetwoIndianisolates,andthreesubstitutionswerefoundatfunctionaldomainsites.Secondarystructurechangesduetothesesubstitutionswerealsoreported.ThisstudyrevealsthattheH5N1strainsisolatedfromchickensduring2006birdfluoutbreaksintwoneighboringdistrictsofMaharashtra,Indiaaregeneticallydifferent.