Relative codon adaptation index, a sensitive measure of codon usage bias

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We propose a simple, sensitive measure of synonymous codon usage bias, the Relative Codon Adaptation Index (rCAI), as a way to discriminate better between highly biased and unbiased regions, compared with the widely used Codon Adaptation Index (CAI). CAI is a geometric mean of the relative usage of codons in a gene, and is calculated using the codon usage table trained with a set of highly expressed genes. In contrast, rCAI is computed by subtracting the background codon usage trained with two noncoding frames of highly expressed genes from the codon usage in the coding frame. rCAI has higher signal-to-noise ratio than CAI, considering that noncoding frames would not show codon bias. Translation efficiency and protein abundance correlates comparably or better with rCAI than CAI or other measures such as 'effective number of codons' and 'SCUMBLE offsets'. Within overlapping coding regions, one of the two coding frames dominates in codon usage bias according to rCAI. Presumably, rCAI could substitute CAI in diverse applications.
Publisher
SAGE Publishing
Issue Date
2010-05
Language
English
Article Type
Article
Citation

EVOLUTIONARY BIOINFORMATICS, v.6, no.6, pp.47 - 55

ISSN
1176-9343
DOI
10.4137/ EBO.S4608
URI
http://hdl.handle.net/10203/101456
Appears in Collection
BS-Journal Papers(저널논문)
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2010.05.05 Relative codon adaptation index, a sensitive measure of codon usage (Evol Bioinform 6, 47).pdf(1.37 MB)Download
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