AnewmethodforintrinsicterminatorpredictionbasedonRnall,anRNAlocalsecondarystructurepredictionalgorithmdevelopedrecently,andtwoU-tailscoreschemasaredeveloped.Byoptimizingthreeparameters(thermodynamicenergyofRNAhairpinstructure,U-tailTweight,andU-tailhybridizationenergy),themethodcanrecognize92.25%ofknownterminatorswhilerejecting98.48%ofpredictedRNAlocalsecondarystructuresincodingregions(negativecontrol)asfalseintrinsicterminatorsinE.coll.ThismethodwasappliedtoscanthegenomeofSynechocgccussp.WH8102,andwepredicted266intrinsicterminators,whichincluded232protein-codinggenes,12tRNAgenes,and3rRNAgenes.About17%oftheseterminatorsarelocatedattheendofoperons.Itisalsoidentified8pairsofbiodirectionalterminators.ThemethodforintrinsicterminatorpredictionhasbeenincorporatedintoRnM1,whichisavailableathttp://digbio.missouri.edu/-wanx/Rnall/.
