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)


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

Open Data