The recognition and prediction of σ70 promoters in Escherichia coli K-12

Based on the conservation analysis of the 683 latest experimentally verified σ70-promoter sequences of Escherichia coli K-12, it is found that the conservative hexamers segments in different sites play a key role of promoter regions, a novel position-correlation scoring matrix (PCSM) algorithm for predicting σ70 promoter is presented. The predictive capacity of the algorithm is tested by 10-cross validation test. The results show that the overall prediction accuracies (sensitivity) and specificity are 91% and 81%, respectively. By selecting the 683 experimentally verified σ70 promoters as training set and searching for the complete sequence in E. coli K-12 with 4639221 bp. Results show that the 100% of the 683 experimentally verified σ70 promoters have been identified and some possible promoters are predicted.