Table 2. Overall measures of accuracy obtained in the self-consistency and jackknife tests for the three different decoding algorithms.
| Decoding method | Qβ | Cβ | SOV | TOP | TOPs |
|---|---|---|---|---|---|
| Self-consistency | |||||
| Viterbi | 92.6% (79.9%) | 0.84 (0.62) | 0.93 (0.86) | 12 (12) | 13 (13) |
| N-Best | 92.8% (80.0%) | 0.85 (0.62) | 0.94 (0.86) | 12 (12) | 14 (14) |
| Posterior | 92.2% (80.1%) | 0.84 (0.62) | 0.94 (0.86) | 12 (12) | 15 (15) |
| Jacknife | |||||
| Viterbi | 86.0% (75.6%) | 0.70 (0.53) | 0.82 (0.76) | 9 (10) | 12 (12) |
| N-Best | 86.0% (75.6%) | 0.70 (0.53) | 0.82 (0.76) | 9 (10) | 12 (12) |
| Posterior | 87.5%(77.0%) | 0.74 (0.56) | 0.85 (0.80) | 8 (8) | 11 (11) |
Qβ: percentage of correctly predicted residues (19). Cβ: Matthews Correlation Coefficient (19). SOV: Segment Overlap measure (18). TOP: proteins with correctly predicted topologies (strand localization and orientation of the loops). TOPs: proteins with correctly predicted topologies, with the inclusion of shifted strand predictions. Values in parentheses correspond to the measures of accuracy obtained when using, as observed, the annotations for the transmembrane strands taken from PDB [see also (13)].