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Comparison of codon usage.
But an absolute comparison of codon usage frequency can not take into account the evolutionary pressure to maintain a given amino acid residue at a particular position, for example for protein folding, stability, and/or function.
Comparison of codon frequencies.
Additional file 2: Comparison of codon preference between B. mori and other model organisms.
A similar effect is seen in a comparison of codon usage for the amino acids leucine and serine (Tab. 4).
A holistic observation and comparison of codon usage patterns over different clades of viruses would throw new insights into virus genome explicitly.
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When a large-scale comparison of codon-pair context excluded global genome biases (Figure 6A) it became evident that contexts that were truly produced by translation-driven selection were grouped in negative or positive rules depending on the phylogeny of the organisms.
Table 2 lists the R2s and slopes for between-genome comparisons of codon occurrences (left) and of motif preferences (right).
In this study, we have included both intra-genomic and inter-genomic comparisons of codon usage.
All dN/dS values were calculated from all pairwise sequence comparisons of codon aligned NarJ subfamily members from the same subgroup (ie. narJ to narJ).
Our comparisons of codon bias in both pairs of species suggest that the intensity of selection on synonymous codons has been reduced in the selfing species compared with their outcrossing sibling species.
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