Table 4.
Results of empirical tests of memory and CPU time required by CM structural alignment algorithms on six known structural RNAs of various sizes.
| tRNA | 5S rRNA | SRP RNA | RNase P | SSU rRNA | LSU rRNA | |
|---|---|---|---|---|---|---|
| # of consensus columns | 72 | 116 | 301 | 379 | 1545 | 2898 |
| # of consensus base pairs | 21 | 35 | 89 | 113 | 462 | 794 |
| # of consensus unpaired | 30 | 46 | 123 | 153 | 621 | 1310 |
| CM states (M) | 230 | 357 | 927 | 1176 | 4789 | 9023 |
| bifurcations (B) | 2 | 1 | 4 | 7 | 30 | 65 |
| Maximum extra decks needed | 1 | 1 | 2 | 2 | 3 | 5 |
| Example sequence length (N) | 73 | 120 | 300 | 377 | 1542 | 2904 |
| Full CYK RAM (MB) | 2.6 | 10.7 | 168.9 | 336.7 | 22705.0 | 151349.7 |
| Divide & conquer RAM (MB) | 0.1 | 0.4 | 2.4 | 3.7 | 66.8 | 270.9 |
| Full CYK CPU time (sec) | 0.2 | 0.7 | 12.7 | 28.6 | n.d. | n.d. |
| CYK CPU time, no trace (sec) | 0.1 | 0.6 | 10.4 | 23.8 | 2614.8 | 25151.2 |
| Divide & conquer time (sec) | 0.2 | 0.9 | 22.8 | 37.8 | 3594.4 | 31649.4 |