CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	RNASLOpt		RDfolder
MCC	0.683	>	0.546
Average MCC ± 95% Confidence Intervals	0.696 ± 0.156	>	0.616 ± 0.181
Sensitivity	0.639	>	0.494
Positive Predictive Value	0.747	>	0.625
Total TP	168	>	130
Total TN	9873	<	9890
Total FP	69	<	82
Total FP CONTRA	19	>	15
Total FP INCONS	38	<	63
Total FP COMP	12	>	4
Total FN	95	<	133
P-value	5.1503931209e-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).
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).
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	0.683
Average MCC ± 95% Confidence Intervals	0.696 ± 0.156
Sensitivity	0.639
Positive Predictive Value	0.747
Nr of predictions	21

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
2LDL_A	-	1.00	1.00	1.00	9	131	1	0	0	1	0
2LK3_A	-	1.00	1.00	1.00	9	91	0	0	0	0	0
3J0L_7	-	-0.02	0.00	0.00	0	506	13	3	10	0	10
3J0L_g	-	-0.01	0.00	0.00	0	174	4	0	2	2	2
3J0L_8	-	0.74	0.57	1.00	4	72	0	0	0	0	3
3J0L_a	-	0.21	0.18	0.29	2	404	6	3	2	1	9
3J0L_1	-	0.73	0.62	0.89	8	475	4	0	1	3	5
3J16_L	tRNA links to Rfam database...	0.63	0.57	0.71	12	1142	5	0	5	0	9
3J20_0	tRNA links to Rfam database...	0.74	0.76	0.73	16	1197	7	3	3	1	5
3SN2_B	IRE_II links to Rfam database...	0.95	0.92	1.00	11	143	0	0	0	0	1
3TRZ_Z	-	1.00	1.00	1.00	5	87	2	0	0	2	0
3TS0_U	-	1.00	1.00	1.00	6	112	1	0	0	1	0
3TS2_V	-	1.00	1.00	1.00	5	103	0	0	0	0	0
3W3S_B	tRNA-Sec links to Rfam database...	0.90	0.85	0.97	28	1960	2	0	1	1	5
4A4U_A	-	1.00	1.00	1.00	9	96	0	0	0	0	0
4AOB_A	SAM links to Rfam database...	0.31	0.28	0.38	8	1416	13	3	10	0	21
4ATO_G	-	0.36	0.43	0.33	3	211	6	6	0	0	4
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
4HXH_A	-	1.00	1.00	1.00	6	89	0	0	0	0	0

Total Scores
MCC	0.546
Average MCC ± 95% Confidence Intervals	0.616 ± 0.181
Sensitivity	0.494
Positive Predictive Value	0.625
Nr of predictions	21

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
2LDL_A	-	1.00	1.00	1.00	9	131	0	0	0	0	0
2LK3_A	-	1.00	1.00	1.00	9	91	0	0	0	0	0
3J0L_7	-	-0.01	0.00	0.00	0	514	5	1	4	0	10
3J0L_g	-	-0.01	0.00	0.00	0	173	3	2	1	0	2
3J0L_8	-	0.92	0.86	1.00	6	70	0	0	0	0	1
3J0L_a	-	-0.02	0.00	0.00	0	407	4	3	1	0	11
3J0L_1	-	0.73	0.62	0.89	8	475	3	0	1	2	5
3J16_L	tRNA links to Rfam database...	0.26	0.24	0.31	5	1143	11	0	11	0	16
3J20_0	tRNA links to Rfam database...	0.82	0.76	0.89	16	1201	3	1	1	1	5
3SN2_B	IRE_II links to Rfam database...	0.95	0.92	1.00	11	143	0	0	0	0	1
3TRZ_Z	-	1.00	1.00	1.00	5	87	0	0	0	0	0
3TS0_U	-	0.91	0.83	1.00	5	113	0	0	0	0	1
3TS2_V	-	1.00	1.00	1.00	5	103	0	0	0	0	0
3W3S_B	tRNA-Sec links to Rfam database...	0.29	0.27	0.33	9	1962	18	2	16	0	24
4A4U_A	-	1.00	1.00	1.00	9	96	0	0	0	0	0
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
4HXH_A	-	1.00	1.00	1.00	6	89	0	0	0	0	0

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