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Relative Codon Adaptation: A Generic Codon Bias Index for Prediction of Gene Expression

The development of codon bias indices (CBIs) remains an active field of research due to their myriad applications in computational biology. Recently, the relative codon usage bias (RCBS) was introduced as a novel CBI able to estimate codon bias without using a reference set. The results of this new...

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Detalles Bibliográficos
Autores principales: Fox, Jesse M., Erill, Ivan
Formato: Texto
Lenguaje:English
Publicado: Oxford University Press 2010
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2885275/
https://www.ncbi.nlm.nih.gov/pubmed/20453079
http://dx.doi.org/10.1093/dnares/dsq012
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author Fox, Jesse M.
Erill, Ivan
author_facet Fox, Jesse M.
Erill, Ivan
author_sort Fox, Jesse M.
collection PubMed
description The development of codon bias indices (CBIs) remains an active field of research due to their myriad applications in computational biology. Recently, the relative codon usage bias (RCBS) was introduced as a novel CBI able to estimate codon bias without using a reference set. The results of this new index when applied to Escherichia coli and Saccharomyces cerevisiae led the authors of the original publications to conclude that natural selection favours higher expression and enhanced codon usage optimization in short genes. Here, we show that this conclusion was flawed and based on the systematic oversight of an intrinsic bias for short sequences in the RCBS index and of biases in the small data sets used for validation in E. coli. Furthermore, we reveal that how the RCBS can be corrected to produce useful results and how its underlying principle, which we here term relative codon adaptation (RCA), can be made into a powerful reference-set-based index that directly takes into account the genomic base composition. Finally, we show that RCA outperforms the codon adaptation index (CAI) as a predictor of gene expression when operating on the CAI reference set and that this improvement is significantly larger when analysing genomes with high mutational bias.
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spelling pubmed-28852752010-06-15 Relative Codon Adaptation: A Generic Codon Bias Index for Prediction of Gene Expression Fox, Jesse M. Erill, Ivan DNA Res Full Papers The development of codon bias indices (CBIs) remains an active field of research due to their myriad applications in computational biology. Recently, the relative codon usage bias (RCBS) was introduced as a novel CBI able to estimate codon bias without using a reference set. The results of this new index when applied to Escherichia coli and Saccharomyces cerevisiae led the authors of the original publications to conclude that natural selection favours higher expression and enhanced codon usage optimization in short genes. Here, we show that this conclusion was flawed and based on the systematic oversight of an intrinsic bias for short sequences in the RCBS index and of biases in the small data sets used for validation in E. coli. Furthermore, we reveal that how the RCBS can be corrected to produce useful results and how its underlying principle, which we here term relative codon adaptation (RCA), can be made into a powerful reference-set-based index that directly takes into account the genomic base composition. Finally, we show that RCA outperforms the codon adaptation index (CAI) as a predictor of gene expression when operating on the CAI reference set and that this improvement is significantly larger when analysing genomes with high mutational bias. Oxford University Press 2010-06 2010-05-07 /pmc/articles/PMC2885275/ /pubmed/20453079 http://dx.doi.org/10.1093/dnares/dsq012 Text en © The Author 2010. Published by Oxford University Press on behalf of Kazusa DNA Research Institute. http://creativecommons.org/licenses/by-nc/2.5/ This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.5), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Full Papers
Fox, Jesse M.
Erill, Ivan
Relative Codon Adaptation: A Generic Codon Bias Index for Prediction of Gene Expression
title Relative Codon Adaptation: A Generic Codon Bias Index for Prediction of Gene Expression
title_full Relative Codon Adaptation: A Generic Codon Bias Index for Prediction of Gene Expression
title_fullStr Relative Codon Adaptation: A Generic Codon Bias Index for Prediction of Gene Expression
title_full_unstemmed Relative Codon Adaptation: A Generic Codon Bias Index for Prediction of Gene Expression
title_short Relative Codon Adaptation: A Generic Codon Bias Index for Prediction of Gene Expression
title_sort relative codon adaptation: a generic codon bias index for prediction of gene expression
topic Full Papers
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2885275/
https://www.ncbi.nlm.nih.gov/pubmed/20453079
http://dx.doi.org/10.1093/dnares/dsq012
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