|
Ranking of the 10 most negative and 10 most positive residual values in S. cerevisiae, S. pombe and C. albicans contexts |
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| S. cerevisiae |
S. pombe |
C. albicans |
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|
|
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| Context |
Residual |
Context |
Residual |
Context |
Residual |
|
|
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| Most negative values |
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| 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 |
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| 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 |
|
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. | |||||
Moura et al. Genome Biology 2005 6:R28 doi:10.1186/gb-2005-6-3-r28 |
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