The analysis of core promoter sequences based on their chemical features

The biochemical behaviors of promoter sequences are closely associated with their chemical properties and structures. In this study, an approach to the analysis of promoter sequences was developed based on the chemical features in DNA sequences. Utilizing the chemical parameters of nucleotides, a string of character sequence was translated into numerical sequences, and then the profiles of chemical properties in the sequence can be observed, which are helpful to better understanding for the behaviors of the sequence. The proposed approach was applied to the analysis of core promoter sequences of Escherichia coli K-12. Apart from the validation of the motifs at the − 35 and − 10 regions, several possible functional sites were observed, and the interaction mechanism between promoter sequence and RNA Polymerase holoenzyme was explored. The obtained results indicate that the consensus of important chemical features is higher than that of the characters in sequences, and our study could provide biologists some valuable hints.