Codon usage bias

Synonymous codon usage patterns in different parasitic platyhelminth mitochondrial genomes

L. Chen, Yang, D. Y., Liu, T. F., Nong, X., Huang, X., Xie, Y., Fu, Y., Zheng, W. P., Zhang, R. H., Wu, X. H., Gu, X. B., Wang, S. X., Peng, X. R., and Yang, G. Y., Synonymous codon usage patterns in different parasitic platyhelminth mitochondrial genomes, vol. 12, pp. 587-596, 2013.

We analyzed synonymous codon usage patterns of the mitochondrial genomes of 43 parasitic platyhelminth species. The relative synonymous codon usage, the effective number of codons (NC) and the frequency of G+C at the third synonymously variable coding position were calculated. Correspondence analysis was used to determine the major variation trends shaping the codon usage patterns. Among the mitochondrial genomes of 19 trematode species, the GC content of third codon positions varied from 0.151 to 0.592, with a mean of 0.295 ± 0.116.

Mapping codon usage in sequence regions flanking cleavage positions in the hepatitis A virus polyprotein

X. - X. Ma, Feng, Y. - P., Chen, L., Zhao, Y. - Q., Liu, J. - L., Guo, J. - Z., Guo, P. - H., Yang, J. - T., Lu, J. - X., Chen, S. - E., and Ma, Z. - R., Mapping codon usage in sequence regions flanking cleavage positions in the hepatitis A virus polyprotein, vol. 12, pp. 2306-2319, 2013.

To analyze the synonymous codon usage patterns of sequence regions flanking cleavage sites in the hepatitis A virus (HAV) polyprotein, the codon usage bias at codon positions and the synonymous codon usage in the target contexts of 30 virus strains were estimated by two simple methods that were based on the values for relative synonymous codon usage. In addition, the pattern of synonymous codon usage was compared between the genomic sequences in HAV and those of its human host.

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