Table 8.

E. coli LSU rRNA is approximately 3350 nucleotides in length. The longest member of our test-set. The highest ranked Sfold prediction is remarkably poor, resolving just 5.8% of the reference structure.

	E. coli LSU rRNA: Single Sequence Methods
Algorithm	number of bps in reference	number of bps in prediction	True Positives (% sensitivity)	False Positives (% selectivity)	Correlation (%)
RNAfold	839	906	435 (51.8)	430 (50.3)	0.510 (51.1)
Mfold (1)	839	883	458 (54.6)	383 (54.5)	0.545 (54.5)
Mfold (2)	839	892	480 (57.2)	364 (56.9)	0.570 (57.0)
Mfold (3)	839	889	454 (54.1)	392 (53.7)	0.539 (53.9)
Sfold (1)	839	903	49 (5.8)	811 (5.7)	0.057 (5.8)
Sfold (2)	839	878	432 (51.5)	411 (51.2)	0.513 (51.4)
Sfold (3)	839	882	384 (45.8)	463 (45.3)	0.455 (45.6)