Restricting the location of the nucleation region to the 3′-end results in an optimal discrimination between bound and unbound sites. (A) Discrimination D as a function of the length n in three scenarios: (1) unrestricted location of the nucleation region (unrestricted n-mer), (2) location restricted to the 5′-end (5′ n-mer), or (3) location restricted to the 3′-end (3′ n-mer). Statistical significance was evaluated with the unpaired one-sided t-test. (B) Discrimination D as a function of Pcutoff for nucleation regions of different lengths, yet always restricted to the 3′-end of the seed match. Results in panels A and B are based on the PAR-CLIP data set. (C,D) The same analysis as in panels A and B, but for the HITS-CLIP data set.
