The recognition and prediction of sigma70 promoters in Escherichia coli K-12.
Based on the conservation analysis of the 683 latest experimentally verified sigma(70)-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 sigma(70) 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 sigma(70) promoters as training set and searching for the complete sequence in E. coli K-12 with 4639221bp. Results show that the 100% of the 683 experimentally verified sigma(70) promoters have been identified and some possible promoters are predicted.
Li
Qian-Zhong
QZ
Department of Physics, Laboratory of Theoretical Biophysics, College of Sciences and Technology, Inner Mongolia University, Hohhot 010021, China. qzli@imu.edu.cn
Lin
Hao
H
D000465:Algorithms; D001483:Base Sequence; D017124:Conserved Sequence; D048168:Escherichia coli K12 / Q000235:genetics*; D015964:Gene Expression Regulation, Bacterial; D005798:Genes, Bacterial; D023281:Genomics; D008957:Models, Genetic; D011401:Promoter Regions, Genetic; D012680:Sensitivity and Specificity