GraphProt performed well in detecting missing binding sites for all RBPs. Prediction performance was measured using AUROC stemming from a tenfold cross-validation (y-axis) on 24 CLIP-seq sets (x-axis) for GraphProt, RNAcontext and MatrixREDUCE. GraphProt and RNAcontext consider sequence and structure information, whereas MatrixREDUCE is only sequence based. MatrixREDUCE results below 0.5 are not shown. See Additional file 2 for the full table of results. AUROC, area under the receiver operating characteristic curve; CLIP-seq, cross-linking and immunoprecipitation sequencing; HITS-CLIP, high-throughput sequencing of RNA isolated by cross-linking immunoprecipitation; iCLIP, individual-nucleotide resolution cross-linking and immunoprecipitation; PAR-CLIP, photoactivatable-ribonucleoside-enhanced cross-linking and immunoprecipitation; RBP, RNA-binding protein.