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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.