Results of the three indexes for the test sets RES and YEAST are reported.

Two cut-offs, chosen on the basis of more or less stringent criteria, are reported for each of the three scores. These thresholds represent the best trade-off found after ROC plot analyses. The cut-offs are 3, 5 for TS, 0.2, 0.3 for InC, 0.3, 0.4 for AC in RES 40 and YEAST 40 and 0.05, 0.01 for AC in YEAST 100, RES 100 and YEAST 4000. The first value represents the less stringent threshold. Sensitivity (SENS), specificity (SPEC), positive predicted value (PPV), negative predicted value (NPV), and accuracy (ACC) have been calculated for low sequence similarity hits below 40% identity (RES 40 and YEAST 40) and for high sequence similarity hits under 100% identity (RES 100 and YEAST 100). YEAST 4000 refers to the benchmarking subset of 4,000 yeast sequences used to make the comparison with Blast2GO performance (see text for further details).