Table 1. Accuracy of evolutionary superfamily assignment and average execution time of fastSCOP, 3D-BLAST and MAMMOTH on 586 queries in the set SCOP-586
| Query type |
Number of queries (domains) |
Program |
Number of assigned domains |
Assignment accuracy (%) |
Unassigned domain percentage (%) |
Average time per query (s) |
Relative to fastSCOP |
|
| Single domain |
464 query proteins (464 domains) |
3D-BLAST |
464 |
94.4% (95.9%a) |
0% |
1.166 |
0.38 |
|
|
MAMMOTH |
464 |
98.7% (98.7%a) |
0% |
1046.47 |
338.61 |
|
|
fastSCOP |
455 |
98.5% (99.6%a) |
1.94% |
3.09 |
1 |
| Multiple domain |
122 query proteins (272 domains) |
3D-BLAST |
275 |
86.9% |
1.8% |
2.238 |
0.34 |
|
|
MAMMOTH |
238 |
94.1% |
12.5% |
1859.80 |
278.40 |
|
|
fastSCOP without reassignmentb |
214 |
98.6% |
19.48% |
5.11 |
0.76 |
|
|
fastSCOP |
254 |
98% |
6.6% |
6.68 |
1 |
|
aAssignment accuracy at SCOP fold level.
bfastSCOP does not apply the reassignment step, which is step 4 in Figure 1A.
SCOP-586 consists of 586 query proteins, which are in SCOP1.69 but not in SCOP1.67; the search database is SCOP1.67.
Time was measured using a personal computer with an Intel Pentium 2.8 GHz processor with 1024 MB of RAM.