CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	RNASLOpt		RDfolder
MCC	0.556	>	0.396
Average MCC ± 95% Confidence Intervals	0.488 ± 0.183	>	0.350 ± 0.184
Sensitivity	0.450	>	0.302
Positive Predictive Value	0.698	>	0.533
Total TP	134	>	90
Total TN	26359	<	26382
Total FP	60	<	81
Total FP CONTRA	8	>	6
Total FP INCONS	50	<	73
Total FP COMP	2	=	2
Total FN	164	<	208
P-value	2.26346675981e-08

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).
Average Matthews Correlation Coefficients (MCC) with 95% confidence intervals (CIs) were plotted for different RNA families, for which at least 3 members were present in the benchmarking dataset. 'n' denotes the number of MCCs used to calculate the average and CI. 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	0.556
Average MCC ± 95% Confidence Intervals	0.488 ± 0.183
Sensitivity	0.450
Positive Predictive Value	0.698
Nr of predictions	13

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_7	-	-0.01	0.00	0.00	0	1212	13	0	13	0	17
3J0L_g	-	-0.01	0.00	0.00	0	461	4	1	3	0	4
3J16_L	tRNA links to Rfam database...	0.53	0.40	0.71	12	2758	5	0	5	0	18
3J20_0	tRNA links to Rfam database...	0.66	0.57	0.77	17	2828	6	1	4	1	13
3J3D_C	tRNA links to Rfam database...	0.82	0.71	0.95	20	2754	1	0	1	0	8
3W3S_B	tRNA-Sec links to Rfam database...	0.82	0.70	0.97	28	4724	2	0	1	1	12
4AOB_A	SAM links to Rfam database...	0.26	0.19	0.38	8	4350	13	2	11	0	34
4ATO_G	-	0.30	0.30	0.33	3	519	6	2	4	0	7
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
4JRC_A	-	0.83	0.70	1.00	16	1524	0	0	0	0	7

Total Scores
MCC	0.396
Average MCC ± 95% Confidence Intervals	0.350 ± 0.184
Sensitivity	0.302
Positive Predictive Value	0.533
Nr of predictions	13

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_7	-	-0.01	0.00	0.00	0	1220	5	0	5	0	17
3J0L_g	-	-0.01	0.00	0.00	0	462	3	1	2	0	4
3J16_L	tRNA links to Rfam database...	0.22	0.17	0.31	5	2759	11	0	11	0	25
3J20_0	tRNA links to Rfam database...	0.73	0.57	0.94	17	2832	2	0	1	1	13
3J3D_C	tRNA links to Rfam database...	0.72	0.61	0.85	17	2755	3	0	3	0	11
3W3S_B	tRNA-Sec links to Rfam database...	0.27	0.23	0.33	9	4726	18	1	17	0	31
4AOB_A	SAM links to Rfam database...	0.35	0.26	0.48	11	4348	13	1	11	1	31
4ATO_G	-	0.63	0.40	1.00	4	524	0	0	0	0	6
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
4JRC_A	-	0.81	0.65	1.00	15	1525	0	0	0	0	8

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