基于位置关联权重矩阵的大肠杆菌启动子预测

对实验证实的683条大肠杆菌sigma70启动子的序列进行保守性计算分析,获得四个保守的区域:-10区域是启动子最保守的功能元件,-35区域、转录起始位点附近及启动子上游UP单元.从保守区中选取M 6(1)值较大的10个保守位点的六联体频数作为参数、引入伪计数构建位置权重矩阵,利用位置关联打分函数对683条sigma70启动子进行预测.负集分别从编码区和非编码区选取700条序列进行算法检验,获得很好的结果,敏感性分别为91%和90%.进而利用位置关联打分函数对大肠杆菌整条序列进行搜索,获得1567条预测序列.这些序列可能是实验未测定的启动子序列.

A New PCWM for E. coli-K12 Promoter Prediction

According to known knowledge of 683 experimentally confirmed sigma70 promoters,it is found that the conservative hexamers segments in different sites play a key role in promoter regions.A new position correlation-score function (PCSF) algorithm combining with pseudocounts for predicting sigma70 promoter is presented.The ability of prediction for the approach shows that the sensitivity are 91% and 90%,respectively,for coding and non-coding (intergenic spacers) test sets.So the PWM-based algorithm is utilized in stringently scanning E.coli-K12 genome.Results show that all of the 683 experimentally verified sigma70 promoters have been identified and 1567 possible promoters are predicted.These predicted sequences may be the sigma70 promoters which have not been confirmed by experiment.