PARma model for replicate A of the DG75 experiment. The conversion model in red represents the conditional propensity that a base becomes cross-linked given there is a uridine at the corresponding position. Note that the propensity is only known up to a constant factor and arbitrarily scaled to a mode of 1. The blue and green lines illustrate the 3' and 5' cleavage models, respectively. These correspond to the conditional probabilities that the RNase Tl cleavage site is at a certain position or closer to the seed site given that there is a guanine. The model shows that the observations made for a few visually inspected validated target sites are also true globally for many clusters.
Erhard et al. Genome Biology 2013 14:R79 doi:10.1186/gb-2013-14-7-r79