利用位点特异性打分矩阵对大肠杆菌启动子的预测

Prediction of Escherichia coli K-12 promoters using position-specific scoring matrix(PSSM) method

启动子是基因转录起始的一个关键性元件。本研究利用数据库中提供的大肠杆菌启动子数据,基于位点特异性打分矩阵(Position-specific scoring matrix,PSSM)算法建立了大肠杆菌启动子预测方法,并采用ROC曲线对预测结果进行评估。结果显示,本方法对大肠杆菌sigma24、sigma28、sigma32、sigma38、sigma54和sigma70启动子预测的准确度分别达到86%,96%,93%,96%,97%和74%。由于原核生物启动子序列的保守性,可将该方法推广至其他原核生物的启动子预测。

Promoter is an essential element in transcription initiation. In this study,we proposed a method for the promoter prediction based on the position-specific scoring matrix（ PSSM） constructed with the data from Regulon DB database,and evaluated the performance through the receiver operating characteristic（ ROC）. We predicted the Escherichia coli K-12 promoters,the accuracies of predictions for sigma24,sigma28,sigma32,sigma38,sigma54 and sigma70 are 86%,96%,93%,96%,97% and 74%,respectively. Since promoter sequences are conserved among prokaryotes,PSSM could be applied to the prediction of prokaryotic promoters.