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Table 2 The following tables display results of several structure predictions using a variety of algorithms upon data-sets containing either S. cerevisiae tRNA-PHE, E. coli RNase P, E. coli SSU rRNA or E. coli LSU rRNA sequences. Reading columns from left to right we show: prediction method, number of base-pairs in the reference structure, number of base-pairs in the predicted structure, the number of true positive base-pairs in the prediction (% sensitivity as described earlier in parentheses), the number of false positive base-pairs in the prediction (% selectivity as described earlier in parentheses), correlation values are the "Matthews correlation coefficient" (with approximate correlation in parentheses). Each of these MFE-based attempts to predict the famous S. cerevisiae tRNA-PHE structure converges on an alternative lengthy-helix type structure. Adding prior knowledge, such as forcing modified bases in the RNA sequence to be unpaired can produce dramatic improvements.

From: A comprehensive comparison of comparative RNA structure prediction approaches

  S. cerevisiae tRNA-PHE: Single Sequence Methods
Algorithm number of bps in reference number of bps in prediction True Positives (% sensitivity) False Positives (% selectivity) Correlation (%)
RNAfold 18 23 4 (22.2) 16 (20.0) 0.178 (21.1)
Mfold (1) 18 21 4 (22.2) 14 (22.2) 0.191 (22.2)
Mfold (2) 18 22 8 (44.4) 11 (42.1) 0.409 (43.3)
Mfold (3) 18 23 4 (22.2) 16 (20.0) 0.178 (21.1)
Sfold (1) 18 23 4 (22.2) 16 (20.0) 0.178 (21.1)
Sfold (2) 18 23 4 (22.2) 16 (20.0) 0.178 (21.1)
Sfold (3) 18 21 4 (22.2) 14 (22.2) 0.191 (22.2)