Table 6.

E. coli SSU rRNA with a length of approximately 1600 nucleotides is beyond the reach of many structure prediction algorithms such as RNAforester and Dynalign. The minimum free energy methods, however, can produce results.

	E. coli SSU rRNA: Single Sequence Methods
Algorithm	number of bps in reference	number of bps in prediction	True Positives (% sensitivity)	False Positives (% selectivity)	Correlation (%)
RNAfold	468	493	207 (44.2)	271 (43.3)	0.437 (43.8)
Mfold (1)	468	480	240 (51.3)	224 (51.7)	0.515 (51.5)
Mfold (2)	468	487	242 (51.7)	229 (51.4)	0.515 (51.5)
Mfold (3)	468	487	202 (43.2)	273 (42.5)	0.428 (42.8)
Sfold (1)	468	481	232 (49.6)	229 (50.3)	0.499 (49.9)
Sfold (2)	468	499	231 (49.4)	249 (48.1)	0.487 (48.7)
Sfold (3)	468	475	232 (49.6)	230 (50.2)	0.498 (49.9)