TABLE 5.

Accuracy and well-determinedness for RNA sequences without and with constraints derived from experiment

		Unconstrained	Constrainedw
Sequence	Type of data	Sensitivityx	PPV	% MFE base pairs PBP ≥ 0.95	PPV base pairs PBP ≥ 0.95	Shannon entropy	Sensitivity	PPV	% MFE base pairs PBP ≥ 0.95	PPV base pairs PBP ≥ 0.95	Shannon entropy
Dog SRPa	Modificationg,v	18.2	15.8	36.6	27.0	0.432	84.1	74.0	45.9	77.8	0.289
E. coli 5S rRNAb	In vivo modificationh, enzymatici	26.3	25.6	17.9	100	0.355	86.8	89.2	56.8	100	0.113
E. coli SSU rRNAc	Modificationj, enzymatick	39.0	34.6	21.9	83.5	0.547	63.0	57.1	36.1	78.4	0.342
C. vinosum RNase Pd	Modificationl	53.5	51.3	57.1	70.6	0.159	53.5	51.3	58.0	71.0	0.151
B. subtilis RNase Pd	Modificationm	56.3	52.9	38.7	82.6	0.381	56.3	52.9	39.5	83.0	0.339
E. coli RNase Pd	Modificationl	57.3	58.7	41.3	100	0.356	63.7	63.7	40.3	100	0.312
Yeast RNase Pd	Modificationn, enzymaticn	59.3	55.2	38.8	97.8	0.493	70.4	64.4	46.6	89.1	0.331
Tetrahymena	In vivo	65.8	58.1	51.2	68.2	0.156	65.8	58.1	51.2	68.2	0.142
telomerasee	modificationo
Yeast group I intron	Modificationp	78.2	70.5	40.9	100	0.268	77.3	71.3	45.7	100	0.257
Tetrahymena group	In vivo	82.9	75.0	42.4	100	0.368	82.9	75.0	43.1	100	0.351
I intronc	modificationo
T4 td group I intronc	FMN cleavageq	85.0	89.5	47.4	100	0.393	83.8	87.0	67.5	100	0.156
Yeast aI5c group II intronf	Modificationr	86.1	87.0	41.0	100	0.254	77.7	83.1	39.7	100	0.255
C. albicans 5S rRNAb	In vivo modificationh	87.5	84.8	30.3	100	0.378	87.5	84.8	45.5	100	0.280
E. coli 23 LSU rRNA domain 1c	Modifications	88.9	75.2	46.3	95.7	0.239	88.9	75.7	48.6	95.8	0.225
P. littoralis group II intronf	Modificationt	89.7	88.3	47.3	100	0.296	89.7	88.3	35.1	100	0.276
Mouse 5S rRNAb	Modificationu	94.4	89.5	21.1	100	0.385	88.9	84.2	52.6	80.0	0.224
Average		66.8 ± 23.8	63.3 ± 23.4	38.8 ± 11.1	89.1 ± 19.8	0.341 ± 0.108	76.3 ± 12.4	72.5 ± 13.1	47.0 ± 8.7	90.2 ± 11.8	0.253 ± 0.078

Structures derived from comparative sequence analysis were derived from ^aGorodkin et al. 2001, ^bSzymanski et al. 2000, ^cCannone et al. 2002, ^dBrown 1999, ^eRomero and Blackburn 1991, ten Dam et al. 1991, and ^fMichel et al. 1989.

Experimental constraints were derived from ^gAndreazzoli and Gerbi 1991, ^hMathews et al. 2004, ⁱSpeek and Lind 1982, ^jMoazed et al. 1986, ^kKean and Draper 1985, ^lLaGrandeur et al. 1994, ^mOdell et al. 1998, ⁿTranguch et al. 1994, ^oZaug and Cech 1995, ^pDMS modification (Chamberlin and Weeks 2003), ^qBurgstaller et al. 1997, ^rKwakman et al. 1990, ^sEgebjerg et al. 1987, and ^tnative conditions chemical modification (Costa et al. 1998), and ^uMiura et al. 1983.

^vThe experimental constraints from protein-bound RNA were used.

^wFor a base pair to be forced single or double stranded on the basis of enzymatic cleavage, cleavage is required on both sides of a nucleotide by the same enzyme (Mathews et al. 1999b). Strong and moderate chemical modifications are used as constraints when data are stratified by intensity (Mathews et al. 2004).

^xWhen there is more than one structure with the lowest free energy, the first structure predicted by the dynamic programming algorithm is scored.