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 {sigma}70 factor of RNA polymerase. {sigma}70 promoters are ubiquitously used in recombinant DNA technology, but characterizing their strength is demanding in terms of both time and money. Using a well-characterized set of promoters, we trained a multivariate linear regression model and found that the log of the promoter strength is significantly linearly associated with a weighted sum of the -10 and -35 sequence profile scores. It was found that the two regions contributed almost equally to the promoter strength. PromoterPredict accepts -10 and -35 hexamer sequences and returns the predicted promoter strength. It is capable of dynamic learning from user-supplied data to refine the model construction and yield more confident estimates of promoter strength.\n\nAvailabilityOpen source code and a standalone executable with both dynamic model-building and prediction are available (under GNU General Public License 3.0) at https://github.com/PromoterPredict, and require Python 2.7 or greater. PromoterPredict is also available as a web service at https://promoterpredict.com.\n\nContactapalania@scbt.sastra.edu