Table 7.

Performance comparison of PROSITE patterns, Profile HMMs and SCFGs

	Size	Method	Max F1	Pr	Rc	Rc| Pr = 1.0
PS00219	12	PROSITE	0.94	1.00	0.89	0.89
	12	SCFG	1.00	1.00	1.00	1.00
PS00063	16	PROSITE	0.81	1.00	0.81	0.81
	16	Profile HMM	0.95	1.00	0.91	0.91
	16	SCFG	0.71	0.79	0.65	0.29
PS00307	7	PROSITE	0.52	0.36	0.94	0.94
	25	Profile HMM	1.00	1.00	1.00	1.00
	25	SCFG	0.91	1.00	0.84	0.84
MPI phosphatase	-	PROSITE	No PROSITE pattern
	25	Profile HMM	0.96	1.00	0.92	0.92
	25	SCFG	0.94	0.98	0.89	0.85
Zinc finger	10-26	PROSITE	Out of scope
	26	Profile HMM	0.79	0.76	0.82	0.21
	26	SCFG	0.81	0.75	0.87	0.21