Table 5.
Average search time and performance of each program on 50 proteins selected from SCOP95-1.69
| Program | Average time of a query (s) | Average time of a pair alignment (s) | Relative to 3D-BLAST | Correct assignment % | Mean of average precision (%) |
|---|---|---|---|---|---|
| 3D-BLAST | 1.298 | 0.000118 | 1 | 94 | 85.20 |
| PSI-BLAST | 0.483 | 0.0000458 | 0.37 | 84 | 68.16 |
| YAKUSA | 8.880 | 0.0008072 | 6.84 | 90 | 74.86 |
| MAMMOTH | 1834.18 | 0.1667285 | 1413.08 | 100 | 94.01 |
| CE | 22053.32 | 2.0047 | 16990 | 98 | 90.78 |
Time was measured using a personal computer equipped with an Intel Pentium 2.8 GHz processor with 512 Mbytes of RAM memory. SCOP95-1.69 is described in Table 1.