Figure 3

S. cerevisiae genome map of codon context. For visualization purposes the values of the residuals of the 64 × 64 codon context table were converted into a color-coded map in which red represents the negative values (bad context) and green the positive values (good context). The values that are not statistically significant are indicated in black (-3 to +3). The color scale represents the full range of values of residuals for yeast codon context. Fixed codons represent the P-site codons and the 3' context refers to the A-site codons as viewed by the ribosome simulation software module. (a) The yeast complete 3' codon context map shows a diagonal green line, which indicates that most codons prefer themselves as neighbors on their 3' side. The map also indicates that without exception, each codon prefers a defined set of neighbors (green) and avoids others (red). The intensity of red and green indicates the extent of the preference or rejection. (b) Codons that are represented in the map can be visualized by zooming into particular areas of the map (boxed in dark blue in (a)). The order of the fixed and 3' context codons indicated in (b) is predefined in the software module.