Relative Codon Adaptation : A Generic Codon Bias Index for Prediction of Gene Expression
Fox, Jesse M. (University of Maryland Baltimore County. Department of Biological Sciences)
Erill, Ivan (University of Maryland Baltimore County. Department of Biological Sciences)

Data:	2010
Resum:	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.
Drets:	Aquest document està subjecte a una llicència d'ús Creative Commons. Es permet la reproducció total o parcial, la distribució, la comunicació pública de l'obra i la creació d'obres derivades, sempre que no sigui amb finalitats comercials, i sempre que es reconegui l'autoria de l'obra original.
Llengua:	Anglès
Document:	Article ; recerca ; Versió publicada
Matèria:	Codon bias index ; Gene expression ; Codon usage ; Escherichia coli ; Highly expressed genes
Publicat a:	DNA Research, Vol. 17, Issue 3 (June 2010) , p. 185-196, ISSN 1340-2838

DOI: 10.1093/dnares/dsq012
PMID: 20453079

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