Table 1 Running time (seconds) on (l, d)-motif challenge problems
From: A particle swarm optimization-based algorithm for finding gapped motifs
Sequence length | 400 | 500 | 600 | 800 | 1000 | 600 | 600 | 600 | 600 |
|---|---|---|---|---|---|---|---|---|---|
( l, d) | (15,4) | (15,4) | (15,4) | (15,4) | (15,4) | (11,2) | (13,3) | (17,5) | (19,6) |
Weeder | 60 | 125 | 200 | 450 | 900 | - | - | - | - |
Projection | 9 | 23 | 42 | 162 | 418 | 4 | 13 | 94 | 174 |
MotifEnumerator | - | - | - | - | - | 5 | 119 | - | - |
PSO | 18 | 34 | 57 | 137 | 288 | 72 | 58 | 61 | 54 |
GALFP | 100 | 123 | 161 | 212 | 286 | 127 | 137 | 162 | 172 |
GAME | 27 | 30 | 32 | 36 | 41 | 23 | 28 | 34 | 42 |
PSO+ | 1.1 | 3.1 | 3.4 | 7.3 | 19.4 | 4.9 | 10.6 | 2.3 | 3.8 |