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/sup 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.