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

Fox, Jesse M.; Erill, Ivan

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

dc.contributor.author	Fox, Jesse M.
dc.contributor.author	Erill, Ivan
dc.date.accessioned	2021-03-09T16:19:12Z
dc.date.available	2021-03-09T16:19:12Z
dc.date.issued	2010-05-07
dc.description.abstract	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.	en_US
dc.description.sponsorship	Funding was provided by the Department of Biological Sciences at the University of Maryland Baltimore County. We would like to thank Michael C. O'Neill, Mauricio Bustos and Maricel Kann for their insightful suggestions and discussion. We are thankful to Michael C. O'Neill for his judicious comments on the manuscript. We thank Patrick O'Farrell for his advice on the methodological basis for biases in proteomic assays.	en_US
dc.description.uri	https://academic.oup.com/dnaresearch/article/17/3/185/354288	en_US
dc.format.extent	12 pages	en_US
dc.genre	journal articles	en_US
dc.identifier	doi:10.13016/m2vgar-wbaz
dc.identifier.citation	Jesse M. Fox, Ivan Erill, Relative Codon Adaptation: A Generic Codon Bias Index for Prediction of Gene Expression, DNA Research, Volume 17, Issue 3, June 2010, Pages 185–196, https://doi.org/10.1093/dnares/dsq012	en_US
dc.identifier.uri	https://doi.org/10.1093/dnares/dsq012
dc.identifier.uri	http://hdl.handle.net/11603/21107
dc.language.iso	en_US	en_US
dc.publisher	Oxford Academic	en_US
dc.relation.isAvailableAt	The University of Maryland, Baltimore County (UMBC)
dc.relation.ispartof	UMBC Biological Sciences Department Collection
dc.relation.ispartof	UMBC Faculty Collection
dc.relation.ispartof	UMBC Student Collection
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dc.rights	Attribution-NonCommercial 2.5 Generic	*
dc.rights.uri	https://creativecommons.org/licenses/by-nc/2.5/	*
dc.title	Relative Codon Adaptation: A Generic Codon Bias Index for Prediction of Gene Expression	en_US
dc.type	Text	en_US