Evaluation of plant miRNA target prediction tools for identifying true miRNA-mRNA interaction in non-Arabidopsis species. (A) Comparison of ‘precision’ and ‘recall’ of the six plant specific tools to optimize scores for predicting targets in non-Arabidopsis dataset. (B) Comparison of true positive and false positive predictions by 6 tools independently and in-combination. The intersection of psRNATarget and Tapirhybrid (PH, marked with an arrow) delivers the best trade-off between true and false positive rates. Overlap of TP and FN is represented in (C) when the union of Targetfinder and psRNATarget (upper Venn diagram) or the intersection of psRNATarget, Tapirhybrid, and Targetfinder (PHI; lower Venn diagram) of predictions are made. Again, bold and regular numbers represent false positives and true positives respectively.