CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	Afold		RNAwolf
MCC	0.516	>	0.449
Average MCC ± 95% Confidence Intervals	0.498 ± 0.317	>	0.414 ± 0.281
Sensitivity	0.467	>	0.417
Positive Predictive Value	0.578	>	0.491
Total TP	93	>	83
Total TN	27136	>	27128
Total FP	84	<	99
Total FP CONTRA	7	<	11
Total FP INCONS	61	<	75
Total FP COMP	16	>	13
Total FN	106	<	116
P-value	0.0

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	0.516
Average MCC ± 95% Confidence Intervals	0.498 ± 0.317
Sensitivity	0.467
Positive Predictive Value	0.578
Nr of predictions	7

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
3J0L_7	-	-0.01	0.00	0.00	0	1210	15	1	14	0	17
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
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

Total Scores
MCC	0.449
Average MCC ± 95% Confidence Intervals	0.414 ± 0.281
Sensitivity	0.417
Positive Predictive Value	0.491
Nr of predictions	7

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
3J0L_7	-	-0.01	0.00	0.00	0	1214	11	0	11	0	17
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
4A1C_2	5_8S_rRNA links to Rfam database...	0.08	0.09	0.08	3	11741	46	10	27	9	30
4ENB_A	crcB links to Rfam database...	0.35	0.32	0.40	6	1260	9	1	8	0	13

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