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.

	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)