Prediction performance with the complete set of features for the three ontologies (a) Molecular function, (b) Cellular component and (c) Biological process. Bars in the left plots show sensitivity and specificity of SVMs. Lines depict geometric mean as a global performance measure for SVM (green) and BLASTP (blue). Right plots depicts variability throughout the five folds of cross-validation. For each ontology, best predicted categories are ordered from top to bottom.