Free energy periodicity in prokaryotic coding and its role in identification of +1 ribosomal frameshifting in the Escherichia Coli K-12 gene prfb

This work reports on a novel signal processing method that can be applied to analysis of genetic sequences in prokaryotes to identify their translational characteristics. The methodology involves computation of a signal based on free-energy score of the interaction between the 3´ tail end of the 16S rRNA and the mRNA sequence of interest. We find that in the coding region of prokaryotes this signal is has a strong harmonic corresponding to every 3^rd base position. Noncoding regions appears not have such a signal. We discuss the methodology in detail and we demonstrate its ability to clearly recognize a) the coding region of a single prokaryotic gene, and b) special characteristics of the gene, such as frameshifts. We use E. Coli K-12 genes to illustrate the findings.