CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	IPknot		RDfolder
MCC	0.625	>	0.423
Average MCC ± 95% Confidence Intervals	0.594 ± 0.244	>	0.370 ± 0.299
Sensitivity	0.574	>	0.355
Positive Predictive Value	0.698	>	0.532
Total TP	81	>	50
Total TN	5627	<	5649
Total FP	37	<	45
Total FP CONTRA	7	<	10
Total FP INCONS	28	<	34
Total FP COMP	2	>	1
Total FN	60	<	91
P-value	0.0

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

Total Scores
MCC	0.625
Average MCC ± 95% Confidence Intervals	0.594 ± 0.244
Sensitivity	0.574
Positive Predictive Value	0.698
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...	0.41	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
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	0.423
Average MCC ± 95% Confidence Intervals	0.370 ± 0.299
Sensitivity	0.355
Positive Predictive Value	0.532
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...	-0.03	0.00	0.00	0	514	14	3	11	0	18
3J0L_a	-	-0.02	0.00	0.00	0	407	4	3	1	0	11
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...	0.35	0.24	0.54	7	1520	6	1	5	0	22
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...	0.48	0.40	0.60	6	462	4	0	4	0	9
4ENC_A	crcB links to Rfam database...	0.48	0.40	0.60	6	486	4	0	4	0	9

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