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：Asystematicphylogeneticfootprintingapproachwasperformedtoidentifycon-servedtranscriptionfactorbindingsites(TFBSs)inmammalianpromoterregionsusinghuman,mouseandratsequencealignments.Wefoundthatthescoredis-tributionsofmostbindingsitemodelsdidnotfollowtheGaussiandistributionrequiredbymanystatisticalmethods.Therefore,weperformedanempiricaltesttoestablishtheoptimalthresholdforeachmodel.WegaugedourcomputationalpredictionsbycomparingwithpreviouslyknownTFBSsinthePCK1genepro-moterofthecytosolicisoformofphosphoenolpyruvatecarboxykinase,andachievedasensitivityof75%andaspecificityofapproximately32%.Almostallknownsitesoverlappedwithpredictedsites,andseveralnewputativeTFBSswerealsoidentified.WevalidatedapredictedSP1bindingsiteinthecontrolofPCK1tran-scriptionusinggelshiftandreporterassays.Finally,weappliedourcomputationalapproachtothepredictionofputativeTFBSswithinthepromoterregionsofallavailableRefSeqgenes.OurfullsetofTFBSpredictionsisfreelyavailableathttp://bfgl.anri.barc.usda.gov/tfbsConsSites.