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Table 8 Frequency of Comparative Base-pairs in 750 Structures Predicted with Mfold 3.1

From: Evaluation of the suitability of free-energy minimization using nearest-neighbor energy parameters for RNA secondary structure prediction

  RNA Contact Distance  
Frequency1 2–100 nt 101–500 nt 501+ nt  
750 21,049 98% 18% 417 2% 2% 0 0% 0% 21,466
600–749 42,362 94% 37% 2,805 6% 14% 33 0% 2% 45,200
151–599 20,775 81% 18% 4,594 18% 23% 266 1% 18% 25,635
1–150 31,285 70% 27% 12,253 27% 61% 1,161 3% 80% 44,699
Correct 115,471 84%   20,069 15%   1,460 1%   137,000
Never 29,587 54%   22,935 42%   2,472 4%   54,994
Total 145,058 76%   43,004 22%   3,932 2%   191,994
  1. For all 496 16S rRNA sequences, a total of 750 structure models are predicted for each sequence (one optimal and 749 suboptimal structure predictions). Every base-pair (excluding any base-pairs involving IUPAC symbols other than A,G,C, or U) in the comparative structure model that appears in a set of 750 structure predictions for a particular sequence is categorized by 1) the number of structure predictions in which it appears and 2) the RNA contact distance. The four bold percentages for each of the three RNA contact distances each total 100%, and reveal the percentage of base-pairs predicted correctly for the four frequency ranges. For example, a total of 115,471 base-pairs with an RNA contact distance of 2–100 nt were predicted correctly. Of those base-pairs, 18% (21,049) were predicted in 750 structure predictions, 37% (42,362) were predicted in 600–749 structure predictions, 18% (20,775) were predicted in 151–599 structure predictions, and 27% (31,285) were predicted in 1–150 structure predictions. In contrast, the three italicized percentages for each of the four frequency ranges, and the "Correct", "Never", and "Total" categories total 100%. For example, 54,994 base-pairs were never predicted in 750 structure predictions. Of those base-pairs, 54% (29,587) have an RNA contact distance of 2–100 nt, 42% (22,935) have an RNA contact distance of 101–500 nt, and 4% (2,472) have an RNA contact distance of 501+ nt.
  2. 1 Frequency of prediction throughout a suboptimal population of up to 750 structure predictions.