Figure 4

Predictions and modeling of the ribosomal density profile based on the features of the coding sequence. (a) Genomic profiles of tAI, folding, charge, a linear regressor based on all these variables, and ribosomal density. In the case of the linear regressor, the predicted ribosomal density is plotted as a function of the distance from the beginning of the ORF (x-axis). The linear regressor is a better predictor of the ribosomal density profile than each of these variables separately (dot plots in Figure S32 in Additional file 2). (b, c) Modeling of ribosomal velocity and density. (b) The velocity of translating the i-th codon is a function of the co-adaptation of the codon to the tRNA pool of the organism, the tAI, the folding energy (FE) after the codon (40 nucleotides), and the charge of the amino acids before the codon (31 amino acids; Materials and methods). (c) To compute the actual velocity we should also consider the initiation and termination times and the fact that a ribosome may be delayed by the ribosome in front of it due to 'traffic jams' (Materials and methods). (d) The profile of ribosomal density (red) versus the predicted profile of translation times based on a deterministic model (green; see (b, c)) and the predicted profile based on a stochastic model (blue; Materials and methods). (e) Correlations of various predictors of ribosomal density with the actual ribosomal density. The predictor that is based on the three variables and the model of ribosomal movement achieved the highest correlation.