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Codon EvolutionMechanisms and Models$
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Gina M. Cannarozzi and Adrian Schneider

Print publication date: 2012

Print ISBN-13: 9780199601165

Published to Oxford Scholarship Online: May 2015

DOI: 10.1093/acprof:osobl/9780199601165.001.0001

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Measuring codon usage bias

Measuring codon usage bias

(p.189) Chapter 13 Measuring codon usage bias
Codon Evolution

Alexander Roth

Maria Anisimova

Gina M. Cannarozzi

Oxford University Press

This chapter introduces the biological causes of codon usage bias and summarizes various indices that have been developed to measure codon bias. It unifies the notation of these codon bias indices to facilitate visualization of their similarities. It also classifies the indices into categories based on historical and methodological similarities. Moreover, the chapter outlines methodologies to evaluate the indices, it evaluates a few indices to illustrate their behaviour, and suggests methodologies for further studies. It examines the dependence of the indices on properties of the sequences using simulations, and estimates the extent to which the indices capture different aspects of expression-based experimental data. Finally, it presents measurement of the correlation of the indices with mRNA and protein abundance data, as well as an estimated rate of synthesis.

Keywords:   codon usage bias, statistical measures, mRNA, protein, simulation, correlation

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