Table 2 Alignment quality results for prob_score and the ProfNet versions trained on different datasets. The ProfNet versions were trained on profile vector pairs from unrelated proteins and protein positions related at family (ProfNet_fam), superfamily (ProfNet_su), fold (ProfNet_fold), and all SCOP levels (ProfNet_all). The training of ProfNet_S was done using superfamily related profile vector pairs as positive examples, and classified by the S-score instead of the binary classifiers used in the other cases. The average MaxSub scores are listed for a test sets with proteins related the family, superfamily or fold levels. The best results are shown in bold.