简介：Withthedevelopmentofgenomesequencingformanyorganisms,moreandmorerawsequencesneedtobeannotated.Genepredictionbycomputationalmethodsforfindingthelocationofproteincodingregionsisoneoftheessentialissuesinbioinformatics.Twoclassesofmethodsaregenerallyadopted:similaritybasedsearchesandabinitioprediction.Here,wereviewthedevelopmentofgenepredictionmethods,summarizethemeasuresforevaluatingpredictorquality,highlightopenproblemsinthisarea,anddiscussfutureresearchdirections.

简介：不同变化(替换)与微妙的还重要的差别当模特儿的为估计在编码蛋白质的序列之中的率采用的同义、非同义的替换的方法，它导致进化信息的不同估计。自从在指向的数据集以内的顺序变化的数量总是是无法预言的，很少注意都没为获得可靠估计被奉献给方法的比较。到我们的知识，几乎没有在关于这些不同方法的评估的文学可得到的很少信息。在这研究，我们比较了六个广泛地使用的方法并且用模仿的序列向结果提供了评估。结果显示那合并顺序特征(例如transition/transversion，偏爱和nucleotide/codon频率偏导)进方法能产出更好的性能。我们建议结论与有关或源于Ka，K分析不应该乐意地从一个方法仅仅根据结果被拉。

简介：Wehavepreviouslydevelopedacombinedsignal/variancedistributionmodelthataccountsfortheparticularstatisticalpropertiesofdatasetsgeneratedontheAp-pliedBiosystemsAB1700transcriptomesystem.Hereweshowthatthismodelcanbeefficientlyusedtogeneratesyntheticdatasetswithstatisticalpropertiesvirtu-allyidenticaltothoseoftheactualdatabyaidoftheJAVAapplicationace.mapcreator1.0thatwehavedeveloped.ThefundamentallydifferentstructureofAB1700transcriptomeprofilesrequiresre-evaluation,adaptation,orevenrede-velopmentofmanyofthestandardmicroarrayanalysismethodsinordertoavoidmisinterpretationofthedataontheonehand,andtodrawfullbenefitfromtheirincreasedspecificityandsensitivityontheotherhand.Ourcompositedatamodelandtheace.mapcreator1.0applicationtherebynotonlypresentproofofthecor-rectnessofourparameterestimation,butalsoprovideatoolforthegenerationofsynthetictestdatathatwillbeusefulforfurtherdevelopmentandtestingofanalysismethods.

简介：Wepresentanintegratedstand-alonesoftwarepackagenamedKaKs_Calculator2.0asanupdatedversion.Itincorporates17methodsforthecalculationofnonsynonymousandsynonymoussubstitutionrates;amongthem,weaddedourmodifiedversionsofseveralwidelyusedmethodsasthegammaseriesincludingγ-NG,γ-LWL,γ-MLWL,γ-LPB,γ-MLPB,γ-YNandγ-MYN,whichhavebeendemonstratedtoperformbetterundercertainconditionsthantheiroriginalformsandarenotimplementedinthepreviousversion.Thepackageisreadilyusedfortheidentificationofpositivelyselectedsitesbasedonaslidingwindowacrossthesequencesofinterestsin5'to3'directionofprotein-codingsequences,andhaveimprovedtheoverallperformanceonsequenceanalysisforevolutionstudies.Atoolbox,includingC++andJavasourcecodeandexecutablefilesonbothWindowsandLinuxplatformstogetherwithauserinstruction,isdownloadablefromthewebsiteforacademicpurposeathttps://sourceforge.net/projects/kakscalculator2/.