Different Patterns of Codon Usage and Amino Acid Composition across Primate Lentiviruses.

Despite these small differences for the AGA and AGG synonyms and for the others, the first principal component identified a clear trend in codon usage ( Figure 2 A).

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This finding suggests that an extension of the study to a wide phylogenetic range of Lentiviruses could reveal the existence of a significant trend in the use of synonymous codons.

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Under the hypothesis that the use of synonyms in HIV-1 could reflect adaptation to that of genes expressed in specific cell types, we found a highly significant correlation between codon usage in HIV-1 and monocytes, which was remarkably higher than that with B and T lymphocytes.

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