CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	IPknot		Cylofold
MCC	0.666	>	0.664
Average MCC ± 95% Confidence Intervals	0.633 ± 0.224	<	0.663 ± 0.246
Sensitivity	0.620	<	0.650
Positive Predictive Value	0.732	>	0.693
Total TP	101	<	106
Total TN	6881	>	6866
Total FP	40	<	49
Total FP CONTRA	9	<	13
Total FP INCONS	28	<	34
Total FP COMP	3	>	2
Total FN	62	>	57
P-value	0.0

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

Total Scores
MCC	0.666
Average MCC ± 95% Confidence Intervals	0.633 ± 0.224
Sensitivity	0.620
Positive Predictive Value	0.732
Nr of predictions	8

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...	0.41	0.33	0.55	6	517	5	1	4	0	12
3J0L_a	-	0.16	0.18	0.18	2	400	10	3	6	1	9
3RKF_A	Purine links to Rfam database...	0.91	0.83	1.00	20	846	0	0	0	0	4
3SD1_A	THF links to Rfam database...	0.74	0.69	0.80	20	1508	5	0	5	0	9
3U4M_B	-	0.91	0.91	0.91	20	1254	3	2	0	1	2
4AOB_A	SAM links to Rfam database...	0.50	0.48	0.54	14	1411	13	3	9	1	15
4ENB_A	crcB links to Rfam database...	0.85	0.73	1.00	11	461	0	0	0	0	4
4ENC_A	crcB links to Rfam database...	0.59	0.53	0.67	8	484	4	0	4	0	7

Total Scores
MCC	0.664
Average MCC ± 95% Confidence Intervals	0.663 ± 0.246
Sensitivity	0.650
Positive Predictive Value	0.693
Nr of predictions	8

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...	0.64	0.61	0.69	11	512	5	1	4	0	7
3J0L_a	-	0.17	0.18	0.20	2	401	9	3	5	1	9
3RKF_A	Purine links to Rfam database...	0.91	0.83	1.00	20	846	0	0	0	0	4
3SD1_A	THF links to Rfam database...	0.71	0.69	0.74	20	1506	7	2	5	0	9
3U4M_B	-	0.49	0.55	0.46	12	1250	14	3	11	0	10
4AOB_A	SAM links to Rfam database...	0.42	0.38	0.48	11	1414	13	3	9	1	18
4ENB_A	crcB links to Rfam database...	1.00	1.00	1.00	15	457	0	0	0	0	0
4ENC_A	crcB links to Rfam database...	0.97	1.00	0.94	15	480	1	1	0	0	0

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