Systematic Survey of Sequence Similarity between Sense and Anti-sense Strands in Escherichia coli Genome

During the last two decades, it is reported that lengthy Anti-sense Overlapping Open Reading Frames (AO-ORFs) exist in the complementary DNA strand of genes. Yomo and coworkers [6] suggest that some “unknown force” is protecting AO-ORFs from mutations generating stop codons. Boldogkoi [1] insists that the AO-ORFs are mere by-products of evolutional processes acting to create special codon usage and base distribution patterns in the coding sequences. Many of these studies have proceeded before the completion of genome projects, and therefore, the discussions have been based on the stop codon distribution and/or relations between the codon usage of genes and the probability to form stop condons for individual genes [1-3, 6]. In this study, we investigate the sequence similarity between sense and anti-sense strands in the whole genome of Escherichia coli systematically to examine whether evolutional significances on the AO-ORFs exist or not and whether locational correlations on the E. coli genome exist or not.