CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	CentroidHomfold‑LAST		Afold
MCC	0.592	>	0.494
Average MCC ± 95% Confidence Intervals	0.508 ± 0.328	>	0.503 ± 0.193
Sensitivity	0.528	>	0.523
Positive Predictive Value	0.674	>	0.479
Total TP	93	>	92
Total TN	13417	>	13363
Total FP	66	<	132
Total FP CONTRA	12	<	25
Total FP INCONS	33	<	75
Total FP COMP	21	<	32
Total FN	83	<	84
P-value	0.0

Comparison of performance of CentroidHomfold-LAST and Afold. 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 CentroidHomfold‑LAST and Afold).
Comparison of average Matthews Correlation Coefficients (MCCs) for CentroidHomfold-LAST and Afold. 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 CentroidHomfold‑LAST and Afold).

Total Scores
MCC	0.592
Average MCC ± 95% Confidence Intervals	0.508 ± 0.328
Sensitivity	0.528
Positive Predictive Value	0.674
Nr of predictions	9

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...	-0.03	0.00	0.00	0	517	11	0	11	0	18
2M58_A	-	-0.01	0.00	0.00	0	539	5	0	5	0	12
3J3E_8	5_8S_rRNA links to Rfam database...	0.07	0.07	0.09	1	2731	16	4	6	6	14
3RKF_A	Purine links to Rfam database...	0.86	0.75	1.00	18	848	0	0	0	0	6
3U4M_B	-	0.78	0.73	0.84	16	1257	4	0	3	1	6
3W3S_B	tRNA-Sec links to Rfam database...	0.94	0.88	1.00	29	1960	1	0	0	1	4
4A1C_2	5_8S_rRNA links to Rfam database...	0.24	0.25	0.24	5	4495	29	8	8	13	15
4ENB_A	crcB links to Rfam database...	0.85	0.73	1.00	11	461	0	0	0	0	4
4JRC_A	-	0.87	0.76	1.00	13	609	0	0	0	0	4

Total Scores
MCC	0.494
Average MCC ± 95% Confidence Intervals	0.503 ± 0.193
Sensitivity	0.523
Positive Predictive Value	0.479
Nr of predictions	9

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...	0.64	0.61	0.69	11	512	6	0	5	1	7
2M58_A	-	0.40	0.42	0.42	5	532	8	1	6	1	7
3J3E_8	5_8S_rRNA links to Rfam database...	0.26	0.33	0.21	5	2718	31	6	13	12	10
3RKF_A	Purine links to Rfam database...	0.91	0.83	1.00	20	846	0	0	0	0	4
3U4M_B	-	0.49	0.55	0.46	12	1250	14	3	11	0	10
3W3S_B	tRNA-Sec links to Rfam database...	0.55	0.55	0.56	18	1957	15	4	10	1	15
4A1C_2	5_8S_rRNA links to Rfam database...	0.19	0.25	0.15	5	4483	43	11	17	15	15
4ENB_A	crcB links to Rfam database...	0.81	0.73	0.92	11	460	3	0	1	2	4
4JRC_A	-	0.27	0.29	0.29	5	605	12	0	12	0	12

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