Table 2.

Comparison of Clustering Results

Data Set	BLASTClust			BAG			SEQOPTICS
	S	P	R	S	P	R	S	P	R
l(Pfam)	0.05	1.00	0.05	0.27	1.00	0.27	0.83	0.99	0.84
2(Pfam)	0.04	1.00	0.04	0.20	1.00	0.20	0.85	0.98	0.87
3(NCBI)	0.11	1.00	0.11	0.60	1.00	0.60	0.66	0.82	0.78
4(Swiss-Prot)	0.06	1.00	0.06	0.50	1.00	0.50	0.81	0.99	0.82

Clustering results of four data sets by three methods according to three parameters: S(Jaccard Coefficient), P(Precision), R(Recall). It shows that SEQOPTICS outperforms BAG and BLASTClust which tend to give more clusters than "true" clusters.