CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	RNASLOpt		RDfolder
MCC	0.392	>	0.229
Average MCC ± 95% Confidence Intervals	0.363 ± 0.240	>	0.175 ± 0.172
Sensitivity	0.299	>	0.168
Positive Predictive Value	0.526	>	0.329
Total TP	50	>	28
Total TN	14010	<	14020
Total FP	45	<	58
Total FP CONTRA	5	=	5
Total FP INCONS	40	<	52
Total FP COMP	0	<	1
Total FN	117	<	139
P-value	0.0

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

Total Scores
MCC	0.392
Average MCC ± 95% Confidence Intervals	0.363 ± 0.240
Sensitivity	0.299
Positive Predictive Value	0.526
Nr of predictions	8

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...	0.47	0.35	0.64	7	1529	4	0	4	0	13
3J0L_a	-	0.26	0.19	0.38	3	1120	5	1	4	0	13
3J0L_g	-	-0.01	0.00	0.00	0	461	4	1	3	0	4
3J0L_7	-	-0.01	0.00	0.00	0	1212	13	0	13	0	17
3J16_L	tRNA links to Rfam database...	0.53	0.40	0.71	12	2758	5	0	5	0	18
4AOB_A	SAM links to Rfam database...	0.26	0.19	0.38	8	4350	13	2	11	0	34
4ENB_A	crcB links to Rfam database...	0.76	0.58	1.00	11	1264	0	0	0	0	8
4ENC_A	crcB links to Rfam database...	0.65	0.47	0.90	9	1316	1	1	0	0	10

Total Scores
MCC	0.229
Average MCC ± 95% Confidence Intervals	0.175 ± 0.172
Sensitivity	0.168
Positive Predictive Value	0.329
Nr of predictions	8

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	1526	14	2	12	0	20
3J0L_a	-	-0.01	0.00	0.00	0	1124	4	1	3	0	16
3J0L_g	-	-0.01	0.00	0.00	0	462	3	1	2	0	4
3J0L_7	-	-0.01	0.00	0.00	0	1220	5	0	5	0	17
3J16_L	tRNA links to Rfam database...	0.22	0.17	0.31	5	2759	11	0	11	0	25
4AOB_A	SAM links to Rfam database...	0.35	0.26	0.48	11	4348	13	1	11	1	31
4ENB_A	crcB links to Rfam database...	0.43	0.32	0.60	6	1265	4	0	4	0	13
4ENC_A	crcB links to Rfam database...	0.43	0.32	0.60	6	1316	4	0	4	0	13

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