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Table 2 Ranking of the 10 most negative and 10 most positive residual values in S. cerevisiae, S. pombe and C. albicans contexts

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

S. cerevisiae   S. pombe   C. albicans  
Context Residual Context Residual Context Residual
Most negative values
UUU → AAG -24.58 GAA → CCU -24.159 UUU → CCA -32.691
GAU → AAG -22.487 GAU → AAG -24.124 UUC → GAA -31.586
AUU → AAA -21.546 UUU → AAG -23.899 UCA → GAU -28.317
AUU → AAG -21.285 AUU → AAA -22.923 AUU → AAG -28.284
CUU → AAA -20.656 UCU → AAG -22.334 GGU → UUU -27.198
UUU → AAA -20.563 CUU → AAA -21.25 AAC → UUA -26.198
UCC → GAA -20.069 GUU → AAA -21.218 GAC → UUA -25.795
AAG → UCU -19.706 AUU → AAG -21.08 UUU → AAG -25.316
GAU → CAA -19.274 UUU → AAA -20.704 GGA → AAA -25.26
GAA → CCA -19.155 GAA → UCU -20.698 UUC → GAU -24.822
Most positive values
GAU → GAU 29.839 CAG → CAA 25.279 ACA → ACA 49.476
AAG → AAG 29.937 GAA → GAG 25.644 CAC → CAC 49.511
UUG → AAA 30.459 AAG → AAG 26.901 CCA → CCA 52.889
GAA → GAA 30.573 CUU → CGU 27.013 GAA → GAA 57.356
AAG → AAA 31.427 GAA → GAA 28.051 AAG → AAA 58.605
CAG → CAA 33.445 AGA → AGA 29.623 GCU → GCU 62.611
AGA → AGA 33.798 AAA → AAG 30.358 ACC → ACC 70.117
GGU → GGU 35.979 GCU → GCU 32.158 GGU → GGU 72.48
GCU → GCU 36.231 GGU → GGU 33.681 AAC → AAC 87.115
CAG → CAG 45.422 UCU → UCU 35.086 CAA → CAA 105.216
  1. Anaconda was used to analyze the codon context of the complete genomes of S. cerevisiae, S. pombe and C. albicans. All possible codon contexts were ranked according to their calculated adjusted residuals, and the 10 most negative and 10 most positive were selected as extreme examples. The results indicate that only a small number of bad or good codon pairs (shown in bold) are shared between all three yeast species.