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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

From: Fold-specific sequence scoring improves protein sequence matching

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
  1. 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)