TABLE 4.

Positive predictive values (PPV) for MFE structure and PPV improvement by centroids over MFE structure

			Average percentage of improvement in PPV with respect to MFE structureb
RNA type	Number of sequences	PPVa of MFE structure	Ensemble centroid	Largest cluster centroid	Best cluster centroid
SSU (16S) rRNA	10	48.10 ± 14.37	14.08 ± 10.67	9.54 ± 11.17	28.31 ± 22.97
LSU (23S) rRNA	10	33.68 ± 13.80	43.86 ± 52.10	36.84 ± 47.51	46.37 ± 43.28
5S rRNA	10	59.78 ± 25.76	26.52 ± 52.76	21.60 ± 57.60	51.42 ± 88.62
Group I intron	9	37.95 ± 20.81	36.37 ± 44.36	20.04 ± 32.99	56.50 ± 57.24
Group II intron	2	29.31 ± 26.14	33.33 ± 4.37	31.55 ± 1.26	32.84 ± 3.09
RNase P	10	42.89 ± 16.49	14.16 ± 18.84	−3.86 ± 37.00	27.99 ± 27.41
SRP RNA	10	77.59 ± 15.83	1.69 ± 13.23	−0.48 ± 15.64	9.63 ± 12.99
tmRNA	10	30.28 ± 19.83	76.78 ± 116.97	39.57 ± 91.33	95.55 ± 122.81
tRNA	10	55.15 ± 20.34	26.49 ± 36.50	15.29 ± 30.62	60.07 ± 44.22
Total	81	47.84 ± 23.28	30.00 ± 55.19	17.64 ± 46.87	46.51 ± 64.02

^aPositive predictive value (PPV) = (number of common base pairs between structure determined by comparative sequence analysis and predicted structure)/(number of base pairs in predicted structure) × 100%.

^bPPV improvement by a centroid with respect to the MFE structure = [(PPV of centroid)/(PPV of MFE structure) − 1] × 100%.