Table 7 Performance comparison of PROSITE patterns, Profile HMMs and SCFGs
From: A stochastic context free grammar based framework for analysis of protein sequences
| Â | Size | Method | Max F1 | Pr | Rc | Rc| Pr = 1.0 |
|---|---|---|---|---|---|---|
PS00219 | 12 | PROSITE | 0.94 | 1.00 | 0.89 | 0.89 |
| Â | 12 | SCFG | 1.00 | 1.00 | 1.00 | 1.00 |
PS00063 | 16 | PROSITE | 0.81 | 1.00 | 0.81 | 0.81 |
| Â | 16 | Profile HMM | 0.95 | 1.00 | 0.91 | 0.91 |
| Â | 16 | SCFG | 0.71 | 0.79 | 0.65 | 0.29 |
PS00307 | 7 | PROSITE | 0.52 | 0.36 | 0.94 | 0.94 |
| Â | 25 | Profile HMM | 1.00 | 1.00 | 1.00 | 1.00 |
| Â | 25 | SCFG | 0.91 | 1.00 | 0.84 | 0.84 |
MPI phosphatase | - | PROSITE | No PROSITE pattern | |||
| Â | 25 | Profile HMM | 0.96 | 1.00 | 0.92 | 0.92 |
| Â | 25 | SCFG | 0.94 | 0.98 | 0.89 | 0.85 |
Zinc finger | 10-26 | PROSITE | Out of scope | |||
| Â | 26 | Profile HMM | 0.79 | 0.76 | 0.82 | 0.21 |
| Â | 26 | SCFG | 0.81 | 0.75 | 0.87 | 0.21 |