CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	Contrafold		Multilign(seed)
MCC	0.581	>	0.556
Average MCC ± 95% Confidence Intervals	0.574 ± 0.190	>	0.517 ± 0.225
Sensitivity	0.478	>	0.432
Positive Predictive Value	0.713	<	0.723
Total TP	176	>	159
Total TN	50430	<	50457
Total FP	91	>	63
Total FP CONTRA	12	=	12
Total FP INCONS	59	>	49
Total FP COMP	20	>	2
Total FN	192	<	209
P-value	1.49320234536e-07

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

Total Scores
MCC	0.581
Average MCC ± 95% Confidence Intervals	0.574 ± 0.190
Sensitivity	0.478
Positive Predictive Value	0.713
Nr of predictions	10

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...	0.45	0.35	0.58	7	1528	5	2	3	0	13
3J3E_8	5_8S_rRNA links to Rfam database...	0.07	0.06	0.10	2	7483	32	1	17	14	31
3RKF_A	Purine links to Rfam database...	0.73	0.59	0.91	20	2189	2	1	1	0	14
3SD1_A	THF links to Rfam database...	0.57	0.48	0.69	20	3887	9	2	7	0	22
3W1K_J	tRNA-Sec links to Rfam database...	0.87	0.79	0.97	30	4155	1	1	0	0	8
3W3S_B	tRNA-Sec links to Rfam database...	0.89	0.80	1.00	32	4721	1	0	0	1	8
3ZEX_C	5_8S_rRNA links to Rfam database...	0.28	0.21	0.38	11	14167	22	3	15	4	41
4AOB_A	SAM links to Rfam database...	0.44	0.36	0.56	15	4344	13	1	11	1	27
4FRN_A	AdoCbl-variant links to Rfam database...	0.65	0.56	0.77	20	5125	6	1	5	0	16
4JF2_A	preQ1-II links to Rfam database...	0.78	0.61	1.00	19	2831	0	0	0	0	12

Total Scores
MCC	0.556
Average MCC ± 95% Confidence Intervals	0.517 ± 0.225
Sensitivity	0.432
Positive Predictive Value	0.723
Nr of predictions	10

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
3J3E_8	5_8S_rRNA links to Rfam database...	0.13	0.09	0.19	3	7487	13	5	8	0	30
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
3W1K_J	tRNA-Sec links to Rfam database...	0.87	0.79	0.97	30	4155	1	1	0	0	8
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
4JF2_A	preQ1-II links to Rfam database...	0.78	0.61	1.00	19	2831	0	0	0	0	12

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