Figure 2

Predicting 20 in vitro nucleosome positions using the W/S and KS-2009 models. (A) The average W/S score profile (black line) and the average P-center profile for the KS-2009 model (red line) [47]. The nucleosomal DNA sequences (Table 1) are aligned around their dyads (position 0); the average score profiles are ‘symmetrized’ with respect to the dyads. (B) Error distribution for the two models. The error is calculated as a discrepancy between the experimental position and the position with the highest theoretical score in the interval [−5, +5]. The occurrence of a given error is shown as the percentage of total sequences. For example, in the case of the W/S scheme, 50% of the nucleosome positions were predicted exactly and 20% of the positions were predicted with errors of +/−1 bp. The sum of the fractions is 100%. Here and in Figure 3B, Figure 4B, Figure 4D, the interval [−5, +5] is chosen because the prevalent distance between neighboring nucleosomes is ~10 bp [56, 57].