CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	IPknot		Afold
MCC	0.567	>	0.516
Average MCC ± 95% Confidence Intervals	0.514 ± 0.307	>	0.498 ± 0.317
Sensitivity	0.462	<	0.467
Positive Predictive Value	0.702	>	0.578
Total TP	92	<	93
Total TN	27166	>	27136
Total FP	45	<	84
Total FP CONTRA	6	<	7
Total FP INCONS	33	<	61
Total FP COMP	6	<	16
Total FN	107	>	106
P-value	0.0

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

Total Scores
MCC	0.567
Average MCC ± 95% Confidence Intervals	0.514 ± 0.307
Sensitivity	0.462
Positive Predictive Value	0.702
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...	0.40	0.30	0.55	6	1529	5	1	4	0	14
2LKR_A	-	0.84	0.77	0.91	30	6072	4	0	3	1	9
3J0L_7	-	-0.01	0.00	0.00	0	1218	7	0	7	0	17
3RKF_A	Purine links to Rfam database...	0.76	0.59	1.00	20	2191	0	0	0	0	14
3U4M_B	-	0.68	0.54	0.87	20	3137	3	1	2	0	17
4A1C_2	5_8S_rRNA links to Rfam database...	0.17	0.15	0.19	5	11755	26	4	17	5	28
4ENB_A	crcB links to Rfam database...	0.76	0.58	1.00	11	1264	0	0	0	0	8

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

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