Impact of bias discrepancy and amino acid usage on estimates of the effective number of codons used in a gene, and a test for selection on codon usage
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Impact of bias discrepancy and amino acid usage on estimates of the effective number of codons used in a gene, and a test for selection on codon usage. / Fuglsang, Anders.
In: Gene, Vol. 410, No. 1, 2007, p. 82-8.Research output: Contribution to journal › Journal article › Research › peer-review
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TY - JOUR
T1 - Impact of bias discrepancy and amino acid usage on estimates of the effective number of codons used in a gene, and a test for selection on codon usage
AU - Fuglsang, Anders
N1 - Keywords: Amino Acids; Codon; Evolution
PY - 2007
Y1 - 2007
N2 - The effective number of codons (Nc) used in a gene is one of the most commonly used measures of synonymous codon usage bias, owing much of its popularity to the fact that it is species independent and that simulation studies have shown that it is less dependent of gene length than other measures. In this paper I provide a clear and practically meaningful definition of bias discrepancy (BD; when the degree of codon bias varies within a degeneracy class). Moreover I evaluate the impact of BD and amino acid usage on estimates of Nc. It is shown that both factors have a significant effect on accuracy and precision. Both amino acid usage and BD influence accuracy considerably, especially in short genes. Finally, I demonstrate how the definition of bias discrepancy can be applied to investigate if codon usage is influenced by selection and I discuss this test in relation to the incongruous literature that exists for Buchnera sp. APS and Borrelia burgdorferi.
AB - The effective number of codons (Nc) used in a gene is one of the most commonly used measures of synonymous codon usage bias, owing much of its popularity to the fact that it is species independent and that simulation studies have shown that it is less dependent of gene length than other measures. In this paper I provide a clear and practically meaningful definition of bias discrepancy (BD; when the degree of codon bias varies within a degeneracy class). Moreover I evaluate the impact of BD and amino acid usage on estimates of Nc. It is shown that both factors have a significant effect on accuracy and precision. Both amino acid usage and BD influence accuracy considerably, especially in short genes. Finally, I demonstrate how the definition of bias discrepancy can be applied to investigate if codon usage is influenced by selection and I discuss this test in relation to the incongruous literature that exists for Buchnera sp. APS and Borrelia burgdorferi.
KW - Former Faculty of Pharmaceutical Sciences
U2 - 10.1016/j.gene.2007.12.001
DO - 10.1016/j.gene.2007.12.001
M3 - Journal article
C2 - 18248919
VL - 410
SP - 82
EP - 88
JO - Gene
JF - Gene
SN - 0378-1119
IS - 1
ER -
ID: 14829833