CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	IPknot		Multilign(seed)
MCC	0.604	>	0.526
Average MCC ± 95% Confidence Intervals	0.593 ± 0.173	>	0.483 ± 0.276
Sensitivity	0.455	>	0.402
Positive Predictive Value	0.807	>	0.695
Total TP	121	>	107
Total TN	35988	>	35984
Total FP	34	<	49
Total FP CONTRA	4	<	6
Total FP INCONS	25	<	41
Total FP COMP	5	>	2
Total FN	145	<	159
P-value	0.0

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

Total Scores
MCC	0.604
Average MCC ± 95% Confidence Intervals	0.593 ± 0.173
Sensitivity	0.455
Positive Predictive Value	0.807
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
3RKF_A	Purine links to Rfam database...	0.76	0.59	1.00	20	2191	0	0	0	0	14
3SD1_A	THF links to Rfam database...	0.61	0.48	0.80	20	3891	5	0	5	0	22
3W3S_B	tRNA-Sec links to Rfam database...	0.85	0.75	0.97	30	4722	2	0	1	1	10
3ZEX_C	5_8S_rRNA links to Rfam database...	0.41	0.21	0.79	11	14182	6	1	2	3	41
4AOB_A	SAM links to Rfam database...	0.42	0.33	0.54	14	4345	13	1	11	1	28
4FRN_A	AdoCbl-variant links to Rfam database...	0.69	0.56	0.87	20	5128	3	1	2	0	16

Total Scores
MCC	0.526
Average MCC ± 95% Confidence Intervals	0.483 ± 0.276
Sensitivity	0.402
Positive Predictive Value	0.695
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...	-0.01	0.00	0.00	0	1528	12	1	11	0	20
3RKF_A	Purine links to Rfam database...	0.76	0.59	1.00	20	2191	0	0	0	0	14
3SD1_A	THF links to Rfam database...	0.55	0.45	0.68	19	3888	9	1	8	0	23
3W3S_B	tRNA-Sec links to Rfam database...	0.84	0.73	0.97	29	4723	2	0	1	1	11
3ZEX_C	5_8S_rRNA links to Rfam database...	0.39	0.27	0.58	14	14172	10	3	7	0	38
4AOB_A	SAM links to Rfam database...	0.61	0.45	0.83	19	4348	5	0	4	1	23
4FRN_A	AdoCbl-variant links to Rfam database...	0.24	0.17	0.35	6	5134	11	1	10	0	30

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