Illustration of the proposed definitions. (a) Four nucleosome configurations, which, together with their respective probabilities, constitute a nucleosome organization. (b-d) The derived (b) nucleosome occupancy, (c) absolute positioning and (d) conditional positioning measures. The configuration with a probability of 0.4 is weighed twice as heavily as the other configurations in the derived occupancy (b) and positioning (c, d) measures. Note how the rightmost nucleosome that appears in the same position in two of the four configurations has a relatively low absolute positioning value (0.4 in (c)) but a high conditional positioning value (1 in (d)), whereas the leftmost nucleosome is relatively well positioned by both the absolute and conditional positioning measures (0.6 in (c) and 0.75 in (d)). Also note that owing to the existence of another nucleosome close to the leftmost nucleosome, the rightmost nucleosome has a higher conditional positioning value than the leftmost nucleosome (d), even though the rightmost nucleosome has an overall lower probability across all four nucleosome configurations. Red boxes in (d) represent regions in which the conditional positioning is undefined.
Kaplan et al. Genome Biology 2010 11:140 doi:10.1186/gb-2010-11-11-140