CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	Afold		ContextFold
MCC	0.337	>	0.326
Average MCC ± 95% Confidence Intervals	0.378 ± 0.141	<	0.405 ± 0.177
Sensitivity	0.303	>	0.268
Positive Predictive Value	0.376	<	0.398
Total TP	334	>	295
Total TN	1164084	<	1164232
Total FP	599	>	482
Total FP CONTRA	58	>	39
Total FP INCONS	497	>	407
Total FP COMP	44	>	36
Total FN	767	<	806
P-value	6.0017973759e-06

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

Total Scores
MCC	0.337
Average MCC ± 95% Confidence Intervals	0.378 ± 0.141
Sensitivity	0.303
Positive Predictive Value	0.376
Nr of predictions	18

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
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
3ZEX_F	-	0.00	0.00	0.00	0	2617	12	2	9	1	12
3ZEX_B	-	0.29	0.26	0.32	147	1071922	322	35	276	11	411
3ZEX_H	-	0.18	0.18	0.18	7	9006	33	6	26	1	31
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	0.326
Average MCC ± 95% Confidence Intervals	0.405 ± 0.177
Sensitivity	0.268
Positive Predictive Value	0.398
Nr of predictions	18

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
2M58_A	-	-0.01	0.00	0.00	0	1639	14	0	14	0	17
3J0L_7	-	-0.01	0.00	0.00	0	1212	13	0	13	0	17
3J2C_O	-	0.83	0.70	1.00	44	10252	1	0	0	1	19
3J3E_8	5_8S_rRNA links to Rfam database...	0.00	0.00	0.00	0	7483	29	9	11	9	33
3U4M_B	-	0.75	0.57	1.00	21	3139	0	0	0	0	16
3W3S_B	tRNA-Sec links to Rfam database...	0.79	0.70	0.90	28	4722	4	0	3	1	12
3ZEX_E	-	0.08	0.06	0.10	5	21896	44	5	39	0	72
3ZEX_D	5S_rRNA links to Rfam database...	0.81	0.67	0.97	33	6987	1	0	1	0	16
3ZEX_F	-	0.00	0.00	0.00	0	2617	16	2	9	5	12
3ZEX_B	-	0.19	0.15	0.23	86	1072008	291	21	265	5	472
3ZEX_H	-	0.22	0.21	0.24	8	9011	26	2	24	0	30
4A1C_2	5_8S_rRNA links to Rfam database...	0.20	0.15	0.28	5	11763	26	0	13	13	28
4ATO_G	-	-0.01	0.00	0.00	0	526	2	0	2	0	10
4ENB_A	crcB links to Rfam database...	0.69	0.47	1.00	9	1266	0	0	0	0	10
4FNJ_A	-	0.79	0.63	1.00	10	585	0	0	0	0	6
4JRC_A	-	0.78	0.61	1.00	14	1526	0	0	0	0	9

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