Research
Conservation of tandem stop codons in yeasts
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* Corresponding author: Laura F Landweber lfl@Princeton.edu
1 Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
2 Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA
Genome Biology 2005, 6:R31 doi:10.1186/gb-2005-6-4-r31
Published: 16 March 2005Additional files
Additional File 1:
Table 1, Frequency of stop codons at each codon location following the real stop codons in S. bayanus. Table 2, Frequency of stop codons at each codon location following the real stop codons in S. paradoxus. Table 3, Frequency of stop codons at each codon location following the real stop codons in S. mikatae. Table 4, Frequency of stop codons at each codon location following the real stop codons in C. glabrata.
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Additional File 2:
In-frame UAA+3 is the only codon location significantly over-represented in all the yeast species.
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Additional File 3:
Because here we studied many codon locations simultaneously and used a less restrictive P-value cutoff, it is very important to further examine the biological signals in other yeast species. Therefore, over-represented locations were examined. Only in frame codon location UAA+3 showed the same tendency in all other species. 1. Significant P-values are shown in bold (95% confidence level; p < 0.05). 2. Under-represented positions are shown as "n.a.".
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Additional File 4:
The blue bars represent the percentages of genes with a tandem stop codon in each biological process and the red bars represent the controls - the percentages of genes with a TAA stop codon in the corresponding groups.
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Additional File 5:
The red bars represent the percentages of genes with a tandem stop codon in each biological functional category and the red bars represent the controls - the percentages of genes with a TAA stop codon in the corresponding groups.
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Additional File 6:
The blue bars represent the percentages of genes with a tandem stop codon in each biological component and the red bars represent the controls - the percentages of genes with a TAA stop codon in the corresponding groups.
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Additional File 7:
The red bars represent the frequency of stop codons at each codon location and the blue bars represent the controls - the frequency of stop codons at the corresponding locations downstream of stop codons in non-coding regions.
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Additional File 8:
The red bars represent the frequency of stop codons at each codon location and the blue bars represent the controls - the frequency of stop codons at the corresponding locations downstream of stop codons in non-coding regions.
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Additional File 9:
1. List of genes with a tandem stop codon in S. cerevisiae 2. List of genes with a tandem stop codon in S. bayanus 3. List of genes with a tandem stop codon in S. mikatae 4. List of genes with a tandem stop codon in S. paradoxus 5. List of genes with a tandem stop codon in C. glabrata
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