GC3 distribution in the complete ORFeome of S. cerevisiae and E. coli and its influence on the overall codon-pair context analysis. In order to study the role of mutational bias upon codon-pair context the ORFeomes of both (a,b) S. cerevisiae and (c,d) E. coli were distributed according to the %GC3 of individual ORFs. The GC3 of the S. cerevisiae and E. coli ORFeomes varied between the intervals 11.9-76.7% and 20-89.4%, respectively. For S. cerevisiae, however, most ORFs had a %GC3 between 35 and 40% (light blue bar in (a)), while for E. coli the majority of the ORFs have a %GC3 between 50 and 60% (light blue bars in (c)). Determination of the codon-pair context for the low and high GC3 subgroups permitted identification of their context differences. The computation of the number of residuals that changed their signal (for example, positive to negative) from one subgroup (low GC3) into the other (high GC3) provided a quantitative measure of the role of GC3 on codon-pair context (red bars in (b) and (d)). For both S. cerevisiae and E. coli GC3 bias has a strong effect on codon-pair context for weak residuals (-3 to +3), but no such effect was observed for contexts with the highest residuals (strong context), indicating that GC3 bias is mainly felt in weak codon-pair contexts.