Table 8.
Minimum, Maximum and Average run times (in seconds) for 5 different methods over 100 randomly chosen 5S RNA and tRNA alignments each from [38] and [39].
| tRNA | 5S RNA | |||||
|---|---|---|---|---|---|---|
| Min | Max | Avg | Min | Max | Avg | |
| Dynalign new constraint | 1.0 | 55.0 | 9.98 | 2.0 | 234.0 | 34.38 |
| Dynalign M constraint | 4.0 | 29.0 | 9.39 | 36.0 | 111.0 | 73.07 |
| StemLoc | 3.0 | 1308.0 | 210.16 | 11.0 | 8133.0 | 616.06 |
| Consan | 21.0 | 793.0 | 209.29 | 123.0 | 7330.0 | 1032.84 |
| FOLDALIGN | 14.0 | 76.0 | 30.33 | 181.0 | 822.0 | 349.48 |
A dual-core AMD Opteron®-270 2.0 GHz system with 4 GBytes of main memory running Linux Fedora Core 4 was utilized for the timing experiments.