Table 5.
The e-values of hits for PSI-blast search, profile HMM search and topology based PSI-blast search for topologies not yielding hits for PSI-blast, profile HMMs or both
| E-values | |||
|---|---|---|---|
| Topology | Psi-blast | HMM | Topology psi-blast |
| 1.10.150 | 1.00E-06 | no hit | 8.00E-18 |
| 1.10.238 | 3.00E-03 | no hit | 7.00E-38 |
| 1.10.533 | no hit | 3.30E-17 | 1.00E-30 |
| 1.10.1200 | no hit | 2.80E-05 | 5.00E-11 |
| 1.20.1250 | no hit | 1.10E-20 | 2.00E-44 |
| 2.40.128 | no hit | 3.00E-19 | 2.00E-59 |
| 2.60.40 | no hit | no hit | 1.00E-35 |
| 3.10.20 | no hits | no hit | 9.00E-25 |
| 3.30.420 | no hit | 5.00E-04 | 1.00E-48 |
| 3.30.450 | 3.00E-31 | no hit | 2.00E-52 |
| 3.40.630 | no hit | no hit | 1.00E-40 |
| 3.90.550 | no hit | 1.30E-06 | 1.00E-68 |
The topology based PSI-blast clearly outperforms these popular conventional methods for not only cases where hits were not obtained by conventional methods but for all the cases tested (for results see Additional file 1)