PromoterPredict: sequence-based modelling of Escherichia coli σ⁷⁰ promoter strength yields logarithmic dependence between promoter strength and sequence.

ABSTRACT: We present PromoterPredict, a dynamic multiple regression approach to predict the strength of Escherichia coli promoters binding the σ⁷⁰ factor of RNA polymerase. σ⁷⁰ promoters are ubiquitously used in recombinant DNA technology, but characterizing their strength is demanding in terms of both time and money. We parsed a comprehensive database of bacterial promoters for the -35 and -10 hexamer regions of σ⁷⁰-binding promoters and used these sequences to construct the respective position weight matrices (PWM). Next we used a well-characterized set of promoters to train a multivariate linear regression model and learn the mapping between PWM scores of the -35 and -10 hexamers and the promoter strength. We found that the log of the promoter strength is s

SUBMITTER: Bharanikumar R 

PROVIDER: S-EPMC6228582 | biostudies-literature | 2018

REPOSITORIES: biostudies-literature