Comparison of codon usage measures and their applicability in prediction of microbial gene expressivity

We compared the performance of several commonly used measures and a novel method we introduce in this paper – Measure Independent of Length and Composition (MILC). Large, randomly generated sequence sets were used to test for dependence on (i) sequence length, (ii) overall amount of codon bias and (iii) codon bias discrepancy in the sequences. A derivative of the method, named MELP (MILC-based Expression Level Predictor) can be used to quantitatively predict gene expression levels from genomic data. It was compared to other similar predictors by examining their correlation with actual, experimentally obtained mRNA or protein abundances.We have established that MILC is a generally applicable measure, being resistant to changes in gene length and overall nucleotide composition, and introducing little noise into measurements. Other methods, however, may also be appropriate in certain applications. Our efforts to quantitatively predict gene expression levels in several prokaryotes and unicellular eukaryotes met with varying levels of success, depending on the experimental dataset and predictor used. Out of all methods, MELP and Rainer Merkl's GCB method had the most consistent behaviour. A 'reference set' containing known ribosomal protein genes appears to be a valid starting point for a codon usage-based expressivity prediction.As the numbers of sequenced genes grew, it became evident that synonymous codons are not used equally [1-3]. Codon frequencies were found to vary on 3 levels: between genomes, between genes in the same genome, and within a single gene [4]. Many factors have been shown to influence codon usage patterns, the most important being: (i) overall nucleotide composition of the genome, reflecting mutational biases; (ii) selective forces acting on highly expressed genes to improve efficiency of translation [5]; and (iii) horizontal gene transfer, with transferred genes retaining the codon frequencies of their former host [6]. Connections have also been de