CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	ContextFold		CentroidHomfold‑LAST
MCC	0.601	>	0.515
Average MCC ± 95% Confidence Intervals	0.543 ± 0.159	>	0.442 ± 0.191
Sensitivity	0.483	>	0.365
Positive Predictive Value	0.754	>	0.734
Total TP	193	>	146
Total TN	51821	<	51878
Total FP	81	>	60
Total FP CONTRA	5	=	5
Total FP INCONS	58	>	48
Total FP COMP	18	>	7
Total FN	207	<	254
P-value	2.04409141234e-08

Comparison of performance of ContextFold and CentroidHomfold-LAST. Positive Predictive Value (PPV) is plotted against sensitivity. Each dot represents a single test of each method. See tables below for raw data (individual counts for ContextFold and CentroidHomfold‑LAST).
Comparison of average Matthews Correlation Coefficients (MCCs) for ContextFold and CentroidHomfold-LAST. The whiskers correspond to 95% confidence intervals (CIs). 'n' denotes the number of MCCs used to calculate average MCCs and CIs. See tables below for raw data (individual counts for ContextFold and CentroidHomfold‑LAST).

Total Scores
MCC	0.601
Average MCC ± 95% Confidence Intervals	0.543 ± 0.159
Sensitivity	0.483
Positive Predictive Value	0.754
Nr of predictions	14

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2LC8_A	GP_knot1 links to Rfam database...	0.55	0.50	0.63	10	1524	6	0	6	0	10
2LKR_A	-	0.65	0.56	0.76	22	6076	9	0	7	2	17
3J0L_7	-	-0.01	0.00	0.00	0	1212	13	0	13	0	17
3J0L_2	-	0.64	0.61	0.69	20	6187	11	2	7	2	13
3J0L_g	-	-0.01	0.00	0.00	0	462	3	1	2	0	4
3J0L_a	-	0.71	0.56	0.90	9	1118	1	0	1	0	7
3J16_L	tRNA links to Rfam database...	0.75	0.57	1.00	17	2758	0	0	0	0	13
3U4M_B	-	0.75	0.57	1.00	21	3139	0	0	0	0	16
3UZL_B	tRNA links to Rfam database...	0.72	0.54	0.95	20	3549	1	0	1	0	17
4A1C_2	5_8S_rRNA links to Rfam database...	0.20	0.15	0.28	5	11763	26	0	13	13	28
4A1C_3	5S_rRNA links to Rfam database...	0.78	0.63	0.97	34	7105	1	0	1	0	20
4AOB_A	SAM links to Rfam database...	0.52	0.40	0.68	17	4346	9	1	7	1	25
4ENB_A	crcB links to Rfam database...	0.69	0.47	1.00	9	1266	0	0	0	0	10
4ENC_A	crcB links to Rfam database...	0.65	0.47	0.90	9	1316	1	1	0	0	10

Total Scores
MCC	0.515
Average MCC ± 95% Confidence Intervals	0.442 ± 0.191
Sensitivity	0.365
Positive Predictive Value	0.734
Nr of predictions	14

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2LC8_A	GP_knot1 links to Rfam database...	-0.01	0.00	0.00	0	1529	11	0	11	0	20
2LKR_A	-	0.00	0.00	0.00	0	6101	4	0	4	0	39
3J0L_7	-	0.60	0.41	0.88	7	1217	1	0	1	0	10
3J0L_2	-	0.49	0.24	1.00	8	6208	0	0	0	0	25
3J0L_g	-	0.00	0.00	0.00	0	465	0	0	0	0	4
3J0L_a	-	-0.01	0.00	0.00	0	1125	3	0	3	0	16
3J16_L	tRNA links to Rfam database...	0.75	0.57	1.00	17	2758	0	0	0	0	13
3U4M_B	-	0.58	0.43	0.80	16	3140	4	0	4	0	21
3UZL_B	tRNA links to Rfam database...	0.72	0.54	0.95	20	3549	1	0	1	0	17
4A1C_2	5_8S_rRNA links to Rfam database...	0.16	0.15	0.18	5	11753	29	5	18	6	28
4A1C_3	5S_rRNA links to Rfam database...	0.68	0.56	0.83	30	7104	6	0	6	0	24
4AOB_A	SAM links to Rfam database...	0.71	0.50	1.00	21	4350	1	0	0	1	21
4ENB_A	crcB links to Rfam database...	0.76	0.58	1.00	11	1264	0	0	0	0	8
4ENC_A	crcB links to Rfam database...	0.76	0.58	1.00	11	1315	0	0	0	0	8

Matthews Correlation Coeffient, Sensitivity and Positive Predictive Value have been calculated based on the paper by Gardener & Giegerich, 2004.