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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.

From: A comprehensive comparison of comparative RNA structure prediction approaches

  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)