Skip to main content

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.
Back to article page

BMC Bioinformatics

ISSN: 1471-2105

Contact us