Table 1.

Performance evaluation results (ROC1). Methods compared: Gapped BLAST, PSI-BLAST, prof_sim and prof_ss. For each method, the number of true family-family relationships that are detected before the first false connection occurs, is given (applied individually to each family, and summed over all families in the test set). Results are given for the following types of false connections: possible, suspicious and error (see text for details).

	Number of true	family-family	relationships	detected by
Type of first false-relation	Gapped-BLAST	PSI-BLAST	prof_sim	prof_ss (predicted ss)	prof_ss (true ss)
Different superfamily, same fold ("possible" relationship)	163	189	231	245	391
Different fold, same class ("weak" relationship)	163	191	231	245	398
Different class ("suspicious" relationship)	174	205	253	299	483
Alpha ↔ Beta ("error" relationship)	709	690	1586	1617	1771