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Table 7 Distribution of 16S rRNA Base-pairs Predicted Correctly and Incorrectly

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

  Overall Archaea Bacteria Eucarya
     (C)1 (M) (N)
Comparative 191,994 10,211 83,385 13,406 29,979 55,013
Opt Correct2 81,934 6,376 41,032 6,105 9,459 18,962
Subopt Correct3 137,000 8,570 65,177 10,032 21,201 32,020
Opt Incorrect2 142,023 4,758 49,563 8,603 27,617 51,482
Subopt Incorrect3 2,372,305 101,253 947,197 161,397 472,614 689,844
Opt Accuracy2,4 41% 62% 49% 46% 30% 34%
Subopt Accuracy3,4 71% 84% 78% 75% 71% 59%
Avg Improvement5 30% 21% 29% 30% 41% 24%
Best Prediction6 92% 91% 89% 92% 92% 90%
Max Improvement7 68% 35% 54% 53% 68% 48%
Min Improvement8 10% 10% 12% 12% 14% 11%
  1. All 496 16S rRNA sequences are considered. Each sequence is folded for a population of one optimal and 749 suboptimal structure predictions. 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. Values are calculated by summing the number of unique base-pairs encountered for each sequence that satisfy each particular category (any base-pairs involving IUPAC symbols other than A,G,C, or U are excluded). For example, Subopt Correct is calculated by summing the number of unique, correctly predicted base-pairs encountered in the population of optimal plus suboptimal structure predictions for each of the 496 16S rRNA sequences. Prediction accuracy when including base-pairs predicted correctly in suboptimal structure predictions is also tabulated.
  2. 1 (c), Chloroplast-encoded sequences; (m), Mitochondrial-encoded sequences; (n), Nuclear-encoded sequences.
  3. 2 Considering only the optimal prediction.
  4. 3 Considering the optimal prediction plus up to 749 suboptimal predictions.
  5. 4 Averages calculated on per sequence basis. Please see Per Sequence Averages in Methods.
  6. 5 Average improvement in Mfold secondary structure prediction accuracy when pooling base-pairs from both the optimal prediction and suboptimal predictions.
  7. 6 The highest Mfold secondary structure prediction accuracy for an individual sequence when pooling base-pairs from both the optimal and suboptimal populations.
  8. 7 The largest improvement in Mfold secondary structure prediction accuracy for an individual sequence when pooling base-pairs from both the optimal and suboptimal populations.
  9. 8 The smallest improvement in Mfold secondary structure prediction accuracy for an individual sequence when pooling base-pairs from both the optimal and suboptimal populations.