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Table 5 Accuracy of Base-pairs Predicted with Mfold 3.1 as a Function of RNA Contact Distance

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

  16S rRNA 23S rRNA
RNA Contact Distance 496 Structures 256 Structures
Comparative Total Base-pairs % of Total Total Base-pairs % of Total
Total 191,994 100 178,958 100
2–100 145,058 76 134,085 75
   2–50 121,170 63 106,534 60
   51–100 23,888 12 27,551 15
101+ 46,936 24 44,873 25
   101–500 43,004 22 37,121 21
   501+ 3,932 2 7,752 4
Predicted with Mfold 3.1      
Total 223,957 100 218,908 100
2–100 150,886 67 137,780 63
   2–50 123,708 55 109,078 50
   51–100 27,178 12 28,702 13
101+ 73,071 33 81,128 37
   101–500 43,498 19 44,139 20
   501+ 29,573 13 36,989 17
Correctly Predicted with Mfold 3.1 %C1 %M   %C %M
Total 81,934 43 37 77,888 44 36
2–100 75,763 52 50 67,130 50 49
   2–50 64,651 53 52 54,898 52 50
   51–100 11,202 47 41 12,232 44 43
101+ 6,171 13 8 10,758 24 13
   101–500 5,978 14 14 9,441 25 21
   501+ 193 5 0.7 1,317 17 4
Avg. Percent Correct 2 Current Previous[29] Current Previous[30]
2–100 50 55 47 53
   2–50 52 - 49 -
   51–100 44 - 40 -
101–200 22 15 26 35
201–300 10 14 22 21
301–400 9 13 13 10
401–500 4 12 16 13
501+ 4 - 14 -
  1. All base-pairs predicted in the comparative and the Mfold optimal structure predictions including those base-pairs predicted correctly (any base-pairs with IUPAC symbols other than A,G,C, or U are excluded) are grouped by RNA contact distance for 16S and 23S rRNA. RNA contact distance is defined as the number of nucleotides intervening between the 5' and 3' halves of a base-pair. The determination of the accuracy for the structures predicted with Mfold is described in the Methods section, RNA Secondary Structure Prediction and Prediction Accuracy Calculations.
  2. 1 %C, the percentage of comparatively predicted base-pairs; %M, the percentage of Mfold predicted base-pairs.
  3. 2 The Per Sequence Average (see Per Sequence Average in Methods) percentage of comparative base-pairs in each distance category predicted correctly in the Mfold optimal structure predictions.