Translation initiation efficiency

Translation of foot-and-mouth disease virus RNA: factors influencing alternative AUG selection

J. L. Liu, Ma, Y. H., Xu, J. Y., Chen, Y. X., Chen, S. E., and Ma, Z. R., Translation of foot-and-mouth disease virus RNA: factors influencing alternative AUG selection, vol. 14, pp. 16803-16812, 2015.

The mechanism of alternative AUG usage in foot-and-mouth disease virus is not completely understood. Using simple computational approaches, we evaluated the contributions of overall codon bias, quantitative codon bias, and %GC of the region between the two alternative AUGs, Region-La, as well as the nucleotide bias of the sequence context flanking each AUG with respect to translation initiation efficiency. For all serotypes of this virus, we found that only a small component of the effect of RNA secondary structure on ribosome scanning was due to the low %GC of Region-La.

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