CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	Afold		RNAwolf
MCC	0.348	>	0.218
Average MCC ± 95% Confidence Intervals	0.398 ± 0.140	>	0.281 ± 0.140
Sensitivity	0.312	>	0.203
Positive Predictive Value	0.389	>	0.235
Total TP	354	>	230
Total TN	1166275	>	1166206
Total FP	599	<	787
Total FP CONTRA	58	<	101
Total FP INCONS	497	<	647
Total FP COMP	44	>	39
Total FN	781	<	905
P-value	3.30280588002e-08

Comparison of performance of Afold and RNAwolf. 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 RNAwolf).
Comparison of average Matthews Correlation Coefficients (MCCs) for Afold and RNAwolf. 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 RNAwolf).

Total Scores
MCC	0.348
Average MCC ± 95% Confidence Intervals	0.398 ± 0.140
Sensitivity	0.312
Positive Predictive Value	0.389
Nr of predictions	19

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_B	-	0.29	0.26	0.32	147	1071922	322	35	276	11	411
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
3ZEX_H	-	0.18	0.18	0.18	7	9006	33	6	26	1	31
3ZEX_F	-	0.00	0.00	0.00	0	2617	12	2	9	1	12
4A1C_2	5_8S_rRNA links to Rfam database...	0.14	0.15	0.14	5	11745	43	5	26	12	28
4ATO_G	-	0.32	0.30	0.38	3	520	6	1	4	1	7
4ENB_A	crcB links to Rfam database...	0.67	0.58	0.79	11	1261	3	1	2	0	8
4FNJ_A	-	0.75	0.63	0.91	10	584	1	0	1	0	6
4JRC_A	-	0.24	0.22	0.29	5	1523	12	0	12	0	18

Total Scores
MCC	0.218
Average MCC ± 95% Confidence Intervals	0.281 ± 0.140
Sensitivity	0.203
Positive Predictive Value	0.235
Nr of predictions	19

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...	0.52	0.50	0.56	10	1522	8	0	8	0	10
2LKR_A	-	0.81	0.74	0.88	29	6072	8	0	4	4	10
2M58_A	-	0.51	0.47	0.57	8	1639	6	3	3	0	9
3J0L_7	-	-0.01	0.00	0.00	0	1214	11	0	11	0	17
3J2C_O	-	0.40	0.37	0.44	23	10244	30	0	29	1	40
3J3E_8	5_8S_rRNA links to Rfam database...	0.00	0.00	0.00	0	7470	42	4	29	9	33
3RKF_A	Purine links to Rfam database...	0.72	0.62	0.84	21	2186	4	0	4	0	13
3U4M_B	-	0.44	0.38	0.52	14	3133	13	0	13	0	23
3W3S_B	tRNA-Sec links to Rfam database...	0.68	0.63	0.74	25	4719	10	0	9	1	15
3ZEX_B	-	0.14	0.13	0.15	70	1071902	417	55	353	9	488
3ZEX_E	-	0.00	0.00	0.00	0	21876	69	10	59	0	77
3ZEX_D	5S_rRNA links to Rfam database...	0.20	0.18	0.22	9	6980	32	3	29	0	40
3ZEX_H	-	0.00	0.00	0.00	0	9006	40	8	31	1	38
3ZEX_F	-	-0.01	0.00	0.00	0	2613	20	6	9	5	12
4A1C_2	5_8S_rRNA links to Rfam database...	0.08	0.09	0.08	3	11741	46	10	27	9	30
4ATO_G	-	-0.02	0.00	0.00	0	520	8	1	7	0	10
4ENB_A	crcB links to Rfam database...	0.35	0.32	0.40	6	1260	9	1	8	0	13
4FNJ_A	-	-0.02	0.00	0.00	0	587	8	0	8	0	16
4JRC_A	-	0.58	0.52	0.67	12	1522	6	0	6	0	11

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