简介：Translationinitiationsites(TISs)areimportantsignalsincDNAsequences.InmanypreviousattemptstopredictTISsincDNAsequences,threemajorfactorsaffectthepredictionperformance:thenatureofthecDNAsequencesets,therelevantfeaturesselected,andtheclassificationmethodsused.Inthispaper,weexaminedifferentapproachestoselectandintegraterelevantfeaturesforTISprediction.Thetopselectedsignificantfeaturesincludethefeaturesfromthepositionweightmatrixandthepropensitymatrix,thenumberofnucleotideCinthesequencedownstreamATG,thenumberofdownstreamstopcodons,thenumberofupstreamATGs,andthenumberofsomeaminoacids,suchasaminoacidsAandD.Withthenumericaldatageneratedfromthesefeatures,differentclassificationmethods,includingdecisiontree,naiveBayes,andsupportvectormachine,wereappliedtothreeindependentsequencesets.Theidentifiedsignificantfeatureswerefoundtobebiologicallymeaningful,whiletheexperimentsshowedpromisingresults.

简介：探索真核细胞的抄写因素(TF)的性质有约束力的地点并且决定他们怎么不同于包围DNA序列，我们检验了与DNA有约束力的地点联系的四个特征：G+C内容，模式复杂性，palindromic结构，和Markov定序订。我们规章的主题的分析从TRANSFAC数据库获得了，用酵母内部是的遗传因子的序列背景，表明这四个特征在主题序列显示出可变丰富。例如，主题序列比是背景序列是更可能的有palindromic结构。另外，这些特征对规章的主题紧局部性，显示他们自己是主题序列的一个性质并且没被一般倡导者分享规章的主题在住的“环境”。由根据他们绑在的TF班毁坏主题序列，更特定的协会被识别。最后，当其它例如复杂性丰富，越过检验的种类是通用的时，我们发现一些关联例如G+C内容丰富，是种类特定的。这里提供的定量分析应该增加我们protein-DNA相互作用的理解并且也帮助通过生物信息学便于规章的主题的发现。

简介：Proteinphosphorylationplaysanimportantroleinvariouscellularprocesses.Duetoitshighcomplexity,themechanismneedstobefurtherstudied.Inthelastfewyears,manymethodshavebeencontributedtothisfield,butalmostalloftheminvestigatedthemechanismbasedonproteinsequencesaroundproteinsites.Inthisstudy,weimplementanexplorationbycharacterizingthemicroenvironmentsurroundingphosphorylatedproteinsiteswithamodifiedshellmodel,andobtainsomesignificantpropertiesbytherank-sumtest,suchasthelackofsomeclassesofresidues,atoms,andsecondarystructures.Furthermore,wefindthatthedepletionofsomepropertiesaffectsproteinphosphorylationremarkably.Ourresultssuggestthatitisameaningfuldirectiontoexplorethemechanismofproteinphosphorylationfrommicroenvironmentandweexpectfurtherfindingsalongwiththeincreasingsizeofphosphorylationandproteinstructuredata.

简介：抄写开始地点(TSS)区域与另外的倡导者元素相比显示出更大的可变性。我们被感兴趣由把信息内容用作一项措施寻找它的可变性。我们在这研究注意可变性在与15nt的块相比包围TSS区域的5核苷酸(nt)的块是重要的。这建议可以被包含的实际区域在在尺寸的5-10nt的范围。为Escherichia关口i，我们注意从dinucleotide替换矩阵的信息内容清楚地显示出更好的辨别，建议一些关联的存在。然而，为人，这效果是少得多，并且为老鼠，它实际上是不在的。我们能断定存在短期在TSS区域以内的关联是种类依赖者并且不是通用的。我们进一步观察到在除了TSS的mitochondrial控制元素有另外的可变区域。有效比较能仅仅在块上被做，这也被注意，当单个核苷酸比较不给我们任何可检测的信号时。

简介：VertebrategenomesarecharacterizedwithCpGdeficiency,particularlyforGC-poorregions.TheGCcontent-relatedCpGdeficiencyisprobablycausedbycontext-dependentdeaminationofmethylatedCpGsites.ThishypothesiswasexaminedinthisstudybycomparingnucleotidefrequenciesatCpGflankingpo-sitionsamonginvertebrateandvertebrategenomes.Thefindingisatransitionofnucleotidepreferenceof5'Tto5'Aattheinvertebrate-vertebrateboundary,indi-catingthatalargenumberofCpGsiteswith5TsweredepletedbecauseofglobalDNAmethylationdevelopedinvertebrates.Atgenomelevel,weinvestigatedCpGobserved/expected(obs/exp)valuesin500bpfragments,andfoundthathigherCpGobs/expvalueisshowninGC-poorregionsofinvertebrategenomes(exceptseaurchin)butinGC-richsequencesofvertebrategenomes.WenextcomparedGCcontentatCpGflankingpositionswithgenomicaverage,showingthattheGCcontentislowerthantheaverageininvertebrategenomes,buthigherthanthatinvertebrategenomes.Theseresultsindicatethatalthough5'Tand5'AaredifferentininducingdeaminationofmethylatedCpGsites,GCcontentisevenmoreimportantinaffectingthedeaminationrate.Inallthetests,theresultsofseaurchinaresimilartovertebratesperhapsduetoitsfractionalDNAmethylation.CpGdeficiencyisthereforesuggestedtobemainlyaresultofhighmutationratesofmethylatedCpGsitesinGC-poorregions.

简介：Inthepost-genomicera,identificationofspecificregulatorymotifsortranscrip-tionfactorbindingsites(TFBSs)innon-codingDNAsequences,whichisessentialtoelucidatetranscriptionalregulatorynetworks,hasemergedasanobstaclethatfrustratesmanyresearchers.Consequently,numerousmotifdiscoverytoolsandcorrelateddatabaseshavebeenappliedtosolvingthisproblem.However,theseexistingmethods,basedondifferentcomputationalalgorithms,showdiversemotifpredictionefficiencyinnon-codingDNAsequences.Therefore,understandingthesimilaritiesanddifferencesofcomputationalalgorithmsandenrichingthemotifdiscoveryliteraturesareimportantforuserstochoosethemostappropriateoneamongtheonlineavailabletools.Moreover,therestilllackscrediblecriteriontoassessmotifdiscoverytoolsandinstructionsforresearcherstochoosethebestaccordingtotheirownprojects.Thusintegrationoftherelatedresourcesmightbeagoodapproachtoimproveaccuracyoftheapplication.Recentstudiesintegrateregulatorymotifdiscoverytoolswithexperimentalmethodstoofferacomplemen-taryapproachforresearchers,andalsoprovideamuch-neededmodelforcurrentresearchesontranscriptionalregulatorynetworks.HerewepresentacomparativeanalysisofregulatorymotifdiscoverytoolsforTFBSs.

简介：Transcriptionfactor(TF)bindingtoitsDNAtargetsiteplaysanessentialroleingeneregulation.Thelocation,orientationandspacingoftranscriptionfactorbindingsites(TFBSs)alsoaffectregulatoryfunctionoftheTF.However,hownucleosomalcontextofTFBSsinfluencesTFbindingandsubsequentgeneregulationremainstobeelucidated.Usinggenome-widenucleosomepositioningandTFbindingdatainbuddingyeast,wefoundthatbindingaffinitiesofTFstoDNAtendtodecreasewithincreasingnucleosomeoccupancyoftheassociatedbindingsites.WefurtherdemonstratedthatnucleosomalcontextofbindingsitesiscorrelatedwithgeneregulationofthecorrespondingTF.Nucleosome-depletedTFBSsarelinkedtohighgeneactivityandlowexpressionnoise,whereasnucleosome-coveredTFBSsareassociatedwithlowgeneactivityandhighexpressionnoise.Moreover,nucleosome-coveredTFBSstendtodisruptcoexpressionofthecorrespondingTFtargetgenes.WeconcludethatnucleosomalcontextofbindingsitesinfluencesTFbindingaffinity,subsequentlyaffectingtheregulationofTFsontheirtargetgenes.ThisemphasizestheneedtoincludenucleosomalcontextofTFBSsinmodelinggeneregulation.

简介：PHProteomicDB是一个写PHP的模块在proteomics帮助研究人员用个人网络站点分享二维的电气泳动胶化数据。不技术或除了一些基础，PHP知识是必要的。PHProteomicDB让一个用户友好的政府连接进入并且更新数据。即时地显示胶化特征，胶化图画，和数的胶化点，他们的相关鉴定在蛋白质数据库指向他们的参考页创造网页。模块在http://www.huvec.com/index.php3是自由地可得到的?rub=Download。