CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	RNAwolf		RDfolder
MCC	0.555	>	0.521
Average MCC ± 95% Confidence Intervals	0.500 ± 0.184	<	0.513 ± 0.211
Sensitivity	0.546	>	0.458
Positive Predictive Value	0.583	<	0.612
Total TP	130	>	109
Total TN	10538	<	10583
Total FP	99	>	71
Total FP CONTRA	19	>	16
Total FP INCONS	74	>	53
Total FP COMP	6	>	2
Total FN	108	<	129
P-value	3.02430207705e-07

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

Total Scores
MCC	0.555
Average MCC ± 95% Confidence Intervals	0.500 ± 0.184
Sensitivity	0.546
Positive Predictive Value	0.583
Nr of predictions	12

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...	0.52	0.50	0.56	9	512	7	0	7	0	9
3J0L_a	-	0.14	0.18	0.14	2	397	13	4	8	1	9
3J20_0	tRNA links to Rfam database...	0.54	0.57	0.52	12	1196	12	2	9	1	9
3J3D_C	tRNA links to Rfam database...	0.92	0.95	0.90	18	948	3	2	0	1	1
3RKF_A	Purine links to Rfam database...	0.89	0.83	0.95	20	845	1	0	1	0	4
3SD1_A	THF links to Rfam database...	0.58	0.59	0.59	17	1504	12	2	10	0	12
3W3S_B	tRNA-Sec links to Rfam database...	0.70	0.70	0.72	23	1957	10	0	9	1	10
4AOB_A	SAM links to Rfam database...	0.26	0.24	0.30	7	1414	17	2	14	1	22
4ATO_G	-	-0.03	0.00	0.00	0	213	7	4	3	0	7
4ENB_A	crcB links to Rfam database...	0.45	0.40	0.55	6	461	5	1	4	0	9
4ENC_A	crcB links to Rfam database...	0.34	0.33	0.38	5	483	9	0	8	1	10
4JRC_A	-	0.71	0.65	0.79	11	608	3	2	1	0	6

Total Scores
MCC	0.521
Average MCC ± 95% Confidence Intervals	0.513 ± 0.211
Sensitivity	0.458
Positive Predictive Value	0.612
Nr of predictions	12

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	514	14	3	11	0	18
3J0L_a	-	-0.02	0.00	0.00	0	407	4	3	1	0	11
3J20_0	tRNA links to Rfam database...	0.82	0.76	0.89	16	1201	3	1	1	1	5
3J3D_C	tRNA links to Rfam database...	0.76	0.79	0.75	15	948	5	3	2	0	4
3RKF_A	Purine links to Rfam database...	0.91	0.83	1.00	20	846	0	0	0	0	4
3SD1_A	THF links to Rfam database...	0.35	0.24	0.54	7	1520	6	1	5	0	22
3W3S_B	tRNA-Sec links to Rfam database...	0.29	0.27	0.33	9	1962	18	2	16	0	24
4AOB_A	SAM links to Rfam database...	0.42	0.38	0.48	11	1414	13	3	9	1	18
4ATO_G	-	0.75	0.57	1.00	4	216	0	0	0	0	3
4ENB_A	crcB links to Rfam database...	0.48	0.40	0.60	6	462	4	0	4	0	9
4ENC_A	crcB links to Rfam database...	0.48	0.40	0.60	6	486	4	0	4	0	9
4JRC_A	-	0.94	0.88	1.00	15	607	0	0	0	0	2

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