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Table 3 Average Accuracy of the Optimal RNA Structure Predicted with Mfold 3.1 Grouped by Phylogeny

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

  5S rRNA 16S rRNA 23S rRNA tRNA
  C P1 C P2 C C
Archaea 79 / 98 / 29 68 / 81 / 55 62 / 77 / 51 59 / 74 / 51 58 / 74 / 40 73 / 100 / 32
Bacteria 62 / 94 / 18 56 / 69 / 39 49 / 68 / 21 53 / 66 / 45 49 / 66 / 31 74 / 100 / 0
Eucarya (n)1 75 / 94 / 0 30 / 47 / 10 34 / 50 / 15 41 / 60 / 23 42 / 63 / 21 61 / 100 / 0
Eucarya (c) 67 / 85 / 16 48 / 71 / 32 46 / 71 / 19 39 / 54 / 19 39 / 49 / 21 73 / 100 / 19
Eucarya (m)   31 / 56 / 17 30 / 60 / 5 38 / 57 / 24 30 / 61 / 1  
Eucarya (m)2    31 / 60 / 5    
Eucarya (m)3    33 / 60 / 16    
  1. All values (average/high/low) shown as percentages unless otherwise indicated. 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. C, Current Study; P1, Previous study by the Gutell Lab for 16S rRNA[29]; P2, Previous study by the Gutell Lab for 23S rRNA[30].
  2. 1 (n), Nuclear-encoded sequences; (c), Chloroplast-encoded sequences; (m), Mitochondrial-encoded sequences.
  3. 2 Based on comparative models with 100 or more canonical base-pairs only.
  4. 3 Based on comparative models with 300 or more canonical base-pairs only.