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Translational Selection Is Ubiquitous in Prokaryotes

Figure 1

Comparison of methods for codon usage analysis.

Top left and right. Performance of different classifiers utilizing codon frequencies in discriminating ribosomal protein genes from the rest of representative organism's protein genes. The receiver operating characteristic (ROC) curves show performance of: the Random Forest (RF) classifier [32], and the nearest centroid classifiers built around three distance measures of codon usage: CB, codon bias [33], CAI, codon adaptation index [27], and MILC, measure independent of length and composition [34]. Bottom left. Number of genomes (out of 461) where the column method outperforms the row method based on the area-under-ROC (AUC) statistic, and the rank correlation of the classifiers' per-gene class probabilities with experimental measurements of E. coli cytoplasmic protein abundances. All results were obtained in 4-fold crossvalidation. Bottom right. Dependence of AUCCAI and AUCRF on genomic G+C content; AUCCAI is decreased in genomes with imbalanced G+C.

Figure 1

doi: https://doi.org/10.1371/journal.pgen.1001004.g001