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MBE Advance Access published online on May 5, 2006
Molecular Biology and Evolution, doi:10.1093/molbev/msl009
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© The Author 2006. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oxfordjournals.org
Accepted April 19, 2006

Letter

Accounting for Background Nucleotide Composition When Measuring Codon Usage Bias: Brilliant Idea, Difficult in Practice

Anders Fuglsang 1 *

1 Danish University of Pharmaceutical Sciences, 2 Universitetsparken, DK-2100 Copenhagen Ø, Denmark; Norwegian Medicines Agency, Sven Oftedals Vei 6-8, N-0950 Oslo, Norway

* To whom correspondence should be addressed.
Anders Fuglsang, E-mail: anfu{at}dfuni.dk


  Abstract

The effective number of codons used in a gene is a commonly used measure of codon usage. It varies between 20 and 61 (standard genetic code) and indicates to which degree the entire genetic code is used. It is a drawback of this method that it does not take background composition into account. This led John Novembre to introduce a variant called Nc' (Mol. Biol. Evol. 19 (2002), 1390-1394). In this letter its properties are under the loupe, with special emphasis on phenomena relating to codon homozygosity. A theoretical misunderstanding regarding this estimator is explained in detail, notably Nc' varies between 0 and 61 in stead of 20 and 61 (with the standard genetic code). Practical examples from the genome of Pseudomonas aeruginosa are given which demonstrate that the problem is not just theoretical.


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[Abstract] [Full Text] [PDF]


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