Optimization of Coding Potentials Using Positional Dependence of Nucleotide Frequencies

We study the coding potential of human DNA sequences, using the positional asymmetry function (Dp) and the positional information function (Iq). Both DpandIq are based on the positional dependence of single nucleotide frequencies. We investigate the accuracy ofDp and Iqin distinguishing coding and non-coding DNA as a function of the parametersp and q, respectively, and explore at which parameters poptand qoptbothDp and Iqdistinguish coding and non-coding DNA most accurately. We compare our findings with classically used parameter values and find that optimized coding potentials yield comparable accuracies as classical frame-independent coding potentials trained on prior data. We find that poptand qoptvary only slightly with the sequence length.