Evaluation of splice junction prediction.(A) Comparison of splice recall (y-axis) versus splice false discovery rate (FDR=1-precision, x-axis) on simulation 1 and 2 (see equations 2 and 3 for definitions). For the human data sets, the frequency of predicted novel splices was compared to the frequency of annotated splices for the Ensembl annotation (see text for definitions, Additional file 1: Figure S5 for results for all real-life data sets). Furthermore, the number of identified annotated and novel junctions was evaluated (see Additional file 1: Figure S6 for results for all data sets). To obtain receiver operation characteristic (ROC)-like curves, numbers were also calculated at increasing thresholds on the number of supporting reads for each junction. (B) Number of correctly predicted (true) and incorrectly (false) junctions were compared for all junctions and annotated and novel junctions separately. In contrast to the RGASP evaluation, we also included junctions covered by only 1 read. ROC-like curves were calculated as in A. (A-B) For ContextMap 2 only results using BWA are shown, results for Bowtie and Bowtie 2 can be found in Additional file 1: Figures S5 and S6 (for A) and S7 (for B).