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

Research output: Contribution to journalJournal articlepeer-review

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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 journalJournal articlepeer-review

Harvard

Fuglsang, A 2007, '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', Gene, vol. 410, no. 1, pp. 82-8. https://doi.org/10.1016/j.gene.2007.12.001

APA

Fuglsang, A. (2007). 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. Gene, 410(1), 82-8. https://doi.org/10.1016/j.gene.2007.12.001

Vancouver

Fuglsang A. 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. Gene. 2007;410(1):82-8. https://doi.org/10.1016/j.gene.2007.12.001

Author

Fuglsang, Anders. / 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. In: Gene. 2007 ; Vol. 410, No. 1. pp. 82-8.

Bibtex

@article{b135b9a0ada911debc73000ea68e967b,
title = "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",
abstract = "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.",
keywords = "Former Faculty of Pharmaceutical Sciences",
author = "Anders Fuglsang",
note = "Keywords: Amino Acids; Codon; Evolution",
year = "2007",
doi = "10.1016/j.gene.2007.12.001",
language = "English",
volume = "410",
pages = "82--8",
journal = "Gene",
issn = "0378-1119",
publisher = "Elsevier",
number = "1",

}

RIS

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