CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	HotKnots		RNASLOpt
MCC	0.587	>	0.449
Average MCC ± 95% Confidence Intervals	0.634 ± 0.259	>	0.484 ± 0.218
Sensitivity	0.631	>	0.438
Positive Predictive Value	0.558	>	0.475
Total TP	82	>	57
Total TN	8989	<	9016
Total FP	81	>	73
Total FP CONTRA	25	>	23
Total FP INCONS	40	=	40
Total FP COMP	16	>	10
Total FN	48	<	73
P-value	0.0

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

Total Scores
MCC	0.587
Average MCC ± 95% Confidence Intervals	0.634 ± 0.259
Sensitivity	0.631
Positive Predictive Value	0.558
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...	0.64	0.61	0.69	11	512	5	0	5	0	7
3J0L_a	-	0.55	0.64	0.50	7	397	8	5	2	1	4
3U4M_B	-	0.49	0.55	0.46	12	1250	14	3	11	0	10
4A1C_2	5_8S_rRNA links to Rfam database...	0.19	0.25	0.15	5	4483	42	12	16	14	15
4AOB_A	SAM links to Rfam database...	0.60	0.59	0.63	17	1410	11	4	6	1	12
4ENB_A	crcB links to Rfam database...	1.00	1.00	1.00	15	457	0	0	0	0	0
4ENC_A	crcB links to Rfam database...	0.97	1.00	0.94	15	480	1	1	0	0	0

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.