CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	Contrafold		RNASLOpt
MCC	0.573	>	0.449
Average MCC ± 95% Confidence Intervals	0.607 ± 0.224	>	0.484 ± 0.218
Sensitivity	0.554	>	0.438
Positive Predictive Value	0.605	>	0.475
Total TP	72	>	57
Total TN	9017	>	9016
Total FP	64	<	73
Total FP CONTRA	18	<	23
Total FP INCONS	29	<	40
Total FP COMP	17	>	10
Total FN	58	<	73
P-value	0.0

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

Total Scores
MCC	0.573
Average MCC ± 95% Confidence Intervals	0.607 ± 0.224
Sensitivity	0.554
Positive Predictive Value	0.605
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...	0.46	0.39	0.58	7	516	5	3	2	0	11
3J0L_a	-	0.53	0.55	0.55	6	400	6	3	2	1	5
3U4M_B	-	0.81	0.77	0.85	17	1256	5	0	3	2	5
4A1C_2	5_8S_rRNA links to Rfam database...	0.21	0.25	0.19	5	4489	33	9	13	11	15
4AOB_A	SAM links to Rfam database...	0.53	0.52	0.56	15	1410	13	3	9	1	14
4ENB_A	crcB links to Rfam database...	0.85	0.73	1.00	11	461	1	0	0	1	4
4ENC_A	crcB links to Rfam database...	0.85	0.73	1.00	11	485	1	0	0	1	4

Total Scores
MCC	0.449
Average MCC ± 95% Confidence Intervals	0.484 ± 0.218
Sensitivity	0.438
Positive Predictive Value	0.475
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...	0.48	0.39	0.64	7	517	4	0	4	0	11
3J0L_a	-	0.21	0.18	0.29	2	404	6	3	2	1	9
3U4M_B	-	0.49	0.55	0.46	12	1250	14	3	11	0	10
4A1C_2	5_8S_rRNA links to Rfam database...	0.30	0.40	0.24	8	4482	35	13	13	9	12
4AOB_A	SAM links to Rfam database...	0.31	0.28	0.38	8	1416	13	3	10	0	21
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...	0.73	0.60	0.90	9	486	1	1	0	0	6

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