Selection Criteria | Num Pairs | Lowest % ID | Full Sankoff | Constrained | Time (s) | Memory (MB) |
---|
 |  |  | BP Sens | Align ID | BP Sens | Align ID | Avg | Longest | Avg | Longest |
tRNA subset |
no pins | 184 | 9 | 77 ± 2 | 83 ± 2 | - | - | 570 | 2674 | 255 | 560 |
= 1.0 | 12 | 56 | 88 ± 3 | 92 ± 3 | 88 ± 3 | 92 ± 3 | 97 | 197 | 137 | 226 |
≥ 0.99 | 115 | 35 | 84 ± 2 | 94 ± 1 | 84 ± 2 | 94 ± 1 | 34 | 218 | 69 | 236 |
≥ 0.98 | 124 | 18 | 84 ± 2 | 93 ± 1 | 84 ± 2 | 93 ± 1 | 32 | 240 | 72 | 236 |
≥ 0.95 | 135 | 14 | 83 ± 2 | 91 ± 1 | 82 ± 2 | 91 ± 1 | 32 | 171 | 70 | 232 |
≥ 0.90 | 146 | 10 | 81 ± 2 | 88 ± 2 | 80 ± 2 | 87 ± 2 | 33 | 145 | 72 | 232 |
≥ 0.85 | 152 | 10 | 80 ± 2 | 87 ± 2 | 79 ± 2 | 86 ± 2 | 31 | 241 | 69 | 232 |
≥ 0.80 | 158 | 9 | 80 ± 2 | 86 ± 2 | 79 ± 2 | 85 ± 2 | 31 | 139 | 69 | 214 |
- For higher posterior thresholds, there are fewer sequence pairs in which at least one pin can be identified; the number of sequence pairs that can be pinned and aligned is indicated in the Num Pairs column, and the percent identity of the most dissimilar pair that can be pinned is indicated in the Lowest ID column. For the subset of pairs that can be pinned at a given posterior threshold, we evaluate basepair sensitivity (BP Sens) and alignment identity (Align ID) for full Sankoff (unconstrained) alignment and the Constrained (pinned) alignment. Comparing these numbers within each row indicates the performance impact of the constraints. The average and maximum resource requirements (Time and Memory) are also shown for each posterior cutoff. The performance gain from pins is primarily determined by the number of pins assigned in a sequence pair. For the subset of sequence pairs that can be pinned at all, the average number of pins is largely a function of the window length and somewhat independent of posterior threshold (here W = 20; avg pins = 2.6). The maximum time and memory requirements are typically for a sequence pair in which only a single pin was discovered.