Strategies for measuring evolutionary conservation of RNA secondary structures

Gruber, Andreas R; Bernhart, Stephan H; Hofacker, Ivo L; Washietl, Stefan

doi:10.1186/1471-2105-9-122

BMC Bioinformatics

Table 2 Comparison of different strategies

From: Strategies for measuring evolutionary conservation of RNA secondary structures

		Structural						CLUSTAL W
Method	Variant	Low		Medium		High		Low		Medium		High
Energy based	SCI	0.79	0.32	0.95	0.70	1.00	1.00	0.79	0.31	0.80	0.42	0.90	0.72
	RNAeval	0.82	0.43	0.86	0.45	1.00	0.99	0.82	0.42	0.76	0.32	0.90	0.68
Base-pair distance	consensus	0.80	0.28	0.93	0.56	1.00	0.99	0.79	0.27	0.85	0.40	0.92	0.79
	pairwise	0.83	0.28	0.90	0.54	0.99	0.98	0.83	0.27	0.81	0.40	0.90	0.78
Mountain metric	consensus	0.78	0.34	0.82	0.38	0.92	0.63	0.78	0.34	0.73	0.29	0.80	0.41
	pairwise	0.79	0.29	0.75	0.33	0.76	0.34	0.79	0.29	0.73	0.30	0.75	0.34
Tree editing	consensus, full	0.77	0.32	0.88	0.44	0.99	0.95	0.77	0.32	0.77	0.31	0.86	0.60
	consensus, HIT	0.76	0.30	0.89	0.46	0.99	0.97	0.76	0.28	0.78	0.33	0.87	0.60
	consensus, coarse grained	0.71	0.22	0.81	0.34	0.95	0.73	0.72	0.21	0.74	0.26	0.83	0.45
	consensus, w. coarse grained	0.74	0.26	0.84	0.36	0.98	0.88	0.74	0.25	0.73	0.28	0.82	0.46
	pairwise, full	0.78	0.31	0.77	0.36	0.88	0.63	0.78	0.31	0.75	0.34	0.87	0.56
	pairwise, HIT	0.77	0.27	0.77	0.36	0.90	0.66	0.76	0.26	0.76	0.34	0.89	0.63
	pairwise, coarse grained	0.72	0.16	0.68	0.23	0.74	0.24	0.72	0.16	0.68	0.22	0.78	0.30
	pairwise, w. coarse grained	0.76	0.23	0.71	0.28	0.81	0.41	0.75	0.15	0.71	0.23	0.82	0.35
	pairwise, MiGaL-Layer 0	0.62	0.07	0.61	0.07	0.67	0.06	0.62	0.07	0.60	0.06	0.66	0.04
	pairwise, MiGaL-Layer 1	0.74	0.27	0.68	0.24	0.77	0.33	0.74	0.27	0.68	0.24	0.76	0.33
	pairwise, MiGaL-Layer 2	0.74	0.23	0.70	0.29	0.82	0.42	0.73	0.22	0.69	0.27	0.78	0.37
	pairwise, MiGaL-Layer 3	0.76	0.27	0.71	0.30	0.84	0.49	0.75	0.26	0.71	0.29	0.82	0.47
Ensemble distance	consensus	0.64	0.32	0.61	0.15	0.72	0.25	0.63	0.31	0.60	0.14	0.70	0.24
	pairwise	0.65	0.42	0.61	0.15	0.72	0.26	0.65	0.32	0.61	0.30	0.72	0.31
Mountain metric using base-pair probabilities	consensus	0.48	0.17	0.58	0.27	0.65	0.40	0.50	0.18	0.56	0.24	0.61	0.28
	pairwise	0.78	0.32	0.75	0.34	0.76	0.31	0.79	0.32	0.72	0.30	0.74	0.31
RNApdist-like	consensus	0.76	0.28	0.79	0.37	0.89	0.44	0.76	0.27	0.73	0.30	0.74	0.25
	pairwise	0.75	0.25	0.78	0.36	0.86	0.45	0.75	0.24	0.73	0.28	0.78	0.30

Low, Medium and High refer to the same information content categories as shown in Fig. 2. Each column consists of two numbers: Left: average AUC, Right: sensitivity at 5% false positive rate. Bold numbers indicate the most accurate method in each category.

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