A Fourier Transform of Equal Symbols (FTES) was applied as a spectral density analysis method to identify DNA bases that repeat at any frequency in selected protein-coding genes. The analysis especially focused on identification of bases responsible for the dominant signal at frequency f=1/3 found in all protein-coding genes. The study included homologous sequences from two gene families and multiple unrelated sequences from single organisms. No signal pattern or spectrum specifically characterized either gene family. However, the patterns of bases comprising the signal at f=1/3 suggested the presence of a genome-specific label for protein-coding genes from the same genome. Data suggest that three factors form the informational basis for the signal structure at f=1/3: (1) codon base positional bias; (2) codon preference; and (3) codon arrangement. Quantitative measure of the contribution of each base to the period-3 signal suggests a basis to distinguish protein-coding genes from different organisms. Application of the FTES analysis characterized genes from Escherichia coli as different from the genes from Pseudomonas aeruginosa. Preliminary analyses of genes from these and three other bacteria by artificial neural nets, using FTES parameters, support our suggestion that the period-3 informational structure contains labels for the genomic origins of protein-coding genes. FTES analysis alone or in combination with other informational measures may reveal pathways and processes of gene flow into and through natural systems of microbial cell populations.
