Most of the current codon usage bias computational approaches are only suitable for the comparison of codon usage bias within a single genome. Here we introduce a new informatics method, referred to as synonymous codon usage order (SCUO), to measure synonymous codon usage bias. In this method, we used Shannon informational theory to describe the SCUO of each gene using a value ranging from 0 to 1, with larger values associated with greater codon bias. We compared our method with the codon adaptation index (CAI) method for measuring codon bias in Escherichia coli and Sacharomyces cerevisiae. We also studied the correlation between SCUO and CAI, and the relation of SCUO with gene length and gene function. Finally, we explored the correlation between SCUO and mRNA abundance in Sacharomyces cerevisiae using SAGE expression data.
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