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Table 3 Ranking of the codon pairs that display the highest residual difference between S. cerevisiae, S. pombe and C. albicans

From: Comparative context analysis of codon pairs on an ORFeome scale

S. pombe-S. cerevisiae S. pombe-C. albicans C. albicans-S. cerevisiae
Context Difference Context Difference Context Difference
CAG → CAG 27,798 CAA → CAA 100,639 CAA → CAA 79,38
UUG → AAA 25,266 AAC → AAC 76,716 AAC → AAC 62,939
CUU → CGU 25,168 ACC → ACC 60,208 ACC → ACC 50,735
CAA → CAG 24,507 CCA → CCA 47,603 CCA → CCA 39,196
AAA → AAG 23,593 ACA → ACA 47,359 CAC → CAC 39,032
UUC → AAA 22,86 CAC → CAC 47,175 ACA → ACA 39,029
AAU → AAU 22,021 GGA → AAA 45,043 GGU → GGU 36,501
CAA → CAA 21,259 AAG → AAA 43,994 GGA → UUA 35,81
GUU → CUU 21,194 CAA → CAG 43,927 GGA → AAA 29,786
GAU → GAC 19,483 UCA → UCA 41,533 GUU → GAU 29,753
  1. Anaconda was used to analyze the codon context of the complete genomes of S. cerevisiae, S. pombe and C. albicans. The adjusted residuals of each codon context calculated for each pair of genomes - that is, S. pombe-S. cerevisiae; S. pombe-C. albicans; and C. albicans-S. cerevisiae - were subtracted and the result converted into a positive number by a module calculation. These values were used to rank the respective codon contexts and the 10 highest cases obtained were selected. Among these three yeast species, S. pombe and S. cerevisiae display the lowest differences, with the maximum value of the difference being found for the CAG-CAG pair (27.798). For S. pombe and C. albicans that value reaches 100.639 for the CAA-CAA codon pair. It is noteworthy that the highest difference value for the former pair is lower than the lowest value for the latter in this ranking of context differences. The only codon pair shared between all three yeast pairs is shown in bold.