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)


Gardner and Giegerich BMC Bioinformatics 2004 5:140   doi:10.1186/1471-2105-5-140

Open Data