Methodology article
Comparison of codon usage measures and their applicability in prediction of microbial gene expressivity
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* Corresponding author: Kristian Vlahoviček kristian@icgeb.org
1 Department of Molecular Biology, Division of Biology, Faculty of Science, Zagreb University, Rooseveltov trg 6, 10000 Zagreb, Croatia
2 Protein Structure and Bioinformatics, International Centre for Genetic Engineering and Biotechnology, Padriciano 99, 34012 Trieste, Italy
BMC Bioinformatics 2005, 6:182 doi:10.1186/1471-2105-6-182
Published: 19 July 2005Additional files
Additional File 1:
Rationale behind the length correction of the MILC method, codon frequencies used for testing of codon usage measures, and performance of the expression level predictors. Sheets 1a, 1b and 1c demonstrate, by example, how the chi-square and G scores for amino acids of different degeneracy classes behave when the observed codon counts are small. Sheet 2 contains the codon frequency tables used in testing of the codon usage measures. Sheet 3 describes the performance of the expression level predictors, expressed as Spearman (rank) and Pearson (linear) correlation coefficients of the predicted values and experimentally obtained mRNA/protein abundance data sets.
Format: XLS Size: 73KB Download file
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