CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	Afold		CentroidHomfold‑LAST
MCC	0.424	>	0.388
Average MCC ± 95% Confidence Intervals	0.431 ± 0.172	>	0.372 ± 0.211
Sensitivity	0.373	>	0.263
Positive Predictive Value	0.490	<	0.579
Total TP	187	>	132
Total TN	81626	<	81780
Total FP	225	>	109
Total FP CONTRA	14	>	7
Total FP INCONS	181	>	89
Total FP COMP	30	>	13
Total FN	314	<	369
P-value	7.57172654109e-08

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

Total Scores
MCC	0.424
Average MCC ± 95% Confidence Intervals	0.431 ± 0.172
Sensitivity	0.373
Positive Predictive Value	0.490
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...	0.61	0.55	0.69	11	1524	6	0	5	1	9
2LKR_A	-	0.93	0.87	1.00	34	6071	3	0	0	3	5
2M58_A	-	0.33	0.29	0.38	5	1640	8	1	7	0	12
3J0L_7	-	-0.01	0.00	0.00	0	1210	15	1	14	0	17
3J2C_O	-	0.58	0.49	0.69	31	10251	15	1	13	1	32
3J3E_8	5_8S_rRNA links to Rfam database...	0.17	0.15	0.19	5	7477	31	2	19	10	28
3RKF_A	Purine links to Rfam database...	0.76	0.59	1.00	20	2191	0	0	0	0	14
3U4M_B	-	0.38	0.32	0.46	12	3134	14	0	14	0	25
3W3S_B	tRNA-Sec links to Rfam database...	0.50	0.45	0.56	18	4721	15	1	13	1	22
3ZEX_E	-	0.00	0.00	0.00	0	21892	55	2	51	2	77
3ZEX_D	5S_rRNA links to Rfam database...	0.72	0.61	0.86	30	6986	5	0	5	0	19
4A1C_2	5_8S_rRNA links to Rfam database...	0.14	0.15	0.14	5	11745	43	5	26	12	28
4ENB_A	crcB links to Rfam database...	0.67	0.58	0.79	11	1261	3	1	2	0	8
4JRC_A	-	0.24	0.22	0.29	5	1523	12	0	12	0	18

Total Scores
MCC	0.388
Average MCC ± 95% Confidence Intervals	0.372 ± 0.211
Sensitivity	0.263
Positive Predictive Value	0.579
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
2M58_A	-	-0.01	0.00	0.00	0	1648	5	0	5	0	17
3J0L_7	-	0.60	0.41	0.88	7	1217	1	0	1	0	10
3J2C_O	-	0.00	0.00	0.00	0	10296	0	0	0	0	63
3J3E_8	5_8S_rRNA links to Rfam database...	0.05	0.03	0.08	1	7490	16	1	11	4	32
3RKF_A	Purine links to Rfam database...	0.72	0.53	1.00	18	2193	0	0	0	0	16
3U4M_B	-	0.58	0.43	0.80	16	3140	4	0	4	0	21
3W3S_B	tRNA-Sec links to Rfam database...	0.85	0.73	1.00	29	4724	1	0	0	1	11
3ZEX_E	-	0.00	0.00	0.00	0	21914	33	1	30	2	77
3ZEX_D	5S_rRNA links to Rfam database...	0.75	0.65	0.86	32	6984	5	0	5	0	17
4A1C_2	5_8S_rRNA links to Rfam database...	0.16	0.15	0.18	5	11753	29	5	18	6	28
4ENB_A	crcB links to Rfam database...	0.76	0.58	1.00	11	1264	0	0	0	0	8
4JRC_A	-	0.75	0.57	1.00	13	1527	0	0	0	0	10

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