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)


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

Open Data