Codon adaptation index as a measure of dominating codon bias.
We propose a simple algorithm to detect dominating synonymous codon usage bias in genomes. The algorithm is based on a precise mathematical formulation of the problem that lead us to use the Codon Adaptation Index (CAI) as a 'universal' measure of codon bias. This measure has been previously employed in the specific context of translational bias. With the set of coding sequences as a sole source of biological information, the algorithm provides a reference set of genes which is highly representative of the bias. This set can be used to compute the CAI of genes of prokaryotic and eukaryotic organisms, including those whose functional annotation is not yet available. An important application concerns the detection of a reference set characterizing translational bias which is known to correlate to expression levels; in this case, the algorithm becomes a key tool to predict gene expression levels, to guide regulatory circuit reconstruction, and to compare species. The algorithm detects also leading-lagging strands bias, GC-content bias, GC3 bias, and horizontal gene transfer. The approach is validated on 12 slow-growing and fast-growing bacteria, Saccharomyces cerevisiae, Caenorhabditis elegans and Drosophila melanogaster.


BACKGROUND
http://www.ihes.fr/~materials.
Institut des Hautes Etudes Scientifiques, 35, route de Chartres, 91440 Bures-sur-Yvette, France. carbone@ihes.fr
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Carbone
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Zinovyev
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Képès
D000222:Adaptation, Physiological / Q000235:genetics; D000465:Algorithms; D000818:Animals; D001419:Bacteria / Q000235:genetics; D001483:Base Sequence; D017173:Caenorhabditis elegans / Q000235:genetics; D003062:Codon / Q000235:genetics*; D004331:Drosophila melanogaster / Q000235:genetics*; D020869:Gene Expression Profiling / Q000379:methods*; D005787:Gene Frequency / Q000235:genetics; D014644:Genetic Variation / Q000235:genetics*; D016678:Genome; D008957:Models, Genetic; D015233:Models, Statistical; D015203:Reproducibility of Results; D012441:Saccharomyces cerevisiae / Q000235:genetics; D012680:Sensitivity and Specificity; D016415:Sequence Alignment / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods*
D003062:Codon