Optimization of coding potentials using positional dependence of nucleotide frequencies

We study the coding potential of human DNA sequences, using the positional asymmetry function (D-p) and the positional information function (I-q). Bot h D-p and I-q are based on the positional dependence of single nucleotide f requencies. We investigate the accuracy of D-p and I-q in distinguishing co ding and non-coding DNA as a function of the parameters p and q, respective ly, and explore at which parameters p(opt) and q(opt) both D-p and I-q dist inguish coding and non-coding DNA most accurately. We compare our findings with classically used parameter values and find that optimized coding poten tials yield comparable accuracies as classical frame-independent coding pot entials trained on prior data. We find that p(opt) and q(opt) vary only sli ghtly with the sequence length. (C) 2000 Academic Press.