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Table 2 Varying Pin Selection Posterior Cutoff. Effects of varying the posterior probability cutoff at a fixed window length of 20 nucleotides, for all pairs of tRNA sequences in the test set.

From: Efficient pairwise RNA structure prediction and alignment using sequence alignment constraints

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
  1. 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.