- Sep 2018
Unlike simple k-mer searching, these methods were designed to predict individual RBP binding sites. They go beyond the motif content alone, for instance by taking into account site accessibility (Li et al. 2010; Zhang et al. 2013) or clustering (Akerman et al. 2009; Zhang et al. 2013).
Suggests that RBPmap is a good choice, provided one uses the weighted rank score accounting for clustering and the conservation filter. mCarts by Zhang et al. applied to the ENCODE CLIP data would complement RBPmap, but what would be even better is if ENCODE had already applied it to their data and can provide the binding site predictions.