CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	Vsfold4		RNASLOpt
MCC	0.461	>	0.449
Average MCC ± 95% Confidence Intervals	0.477 ± 0.268	<	0.484 ± 0.218
Sensitivity	0.446	>	0.438
Positive Predictive Value	0.492	>	0.475
Total TP	58	>	57
Total TN	9018	>	9016
Total FP	74	>	73
Total FP CONTRA	14	<	23
Total FP INCONS	46	>	40
Total FP COMP	14	>	10
Total FN	72	<	73
P-value	0.0

Comparison of performance of Vsfold4 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 Vsfold4 and RNASLOpt).
Comparison of average Matthews Correlation Coefficients (MCCs) for Vsfold4 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 Vsfold4 and RNASLOpt).

Total Scores
MCC	0.461
Average MCC ± 95% Confidence Intervals	0.477 ± 0.268
Sensitivity	0.446
Positive Predictive Value	0.492
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	515	13	0	13	0	18
3J0L_a	-	0.39	0.36	0.44	4	402	6	4	1	1	7
3U4M_B	-	0.49	0.55	0.46	12	1250	14	3	11	0	10
4A1C_2	5_8S_rRNA links to Rfam database...	0.36	0.40	0.33	8	4492	28	4	12	12	12
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...	0.77	0.60	1.00	9	487	0	0	0	0	6

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.