CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	Fold		RDfolder
MCC	0.575	>	0.510
Average MCC ± 95% Confidence Intervals	0.497 ± 0.162	<	0.505 ± 0.177
Sensitivity	0.572	>	0.455
Positive Predictive Value	0.595	>	0.592
Total TP	166	>	132
Total TN	13036	<	13092
Total FP	119	>	93
Total FP CONTRA	32	>	19
Total FP INCONS	81	>	72
Total FP COMP	6	>	2
Total FN	124	<	158
P-value	3.415269236e-08

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

Total Scores
MCC	0.575
Average MCC ± 95% Confidence Intervals	0.497 ± 0.162
Sensitivity	0.572
Positive Predictive Value	0.595
Nr of predictions	14

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	513	15	3	12	0	18
3ADB_C	-	0.86	0.85	0.88	28	1787	4	0	4	0	5
3J0L_a	-	0.15	0.18	0.17	2	399	11	4	6	1	9
3J20_0	tRNA links to Rfam database...	0.54	0.57	0.52	12	1196	12	3	8	1	9
3J3D_C	tRNA links to Rfam database...	0.47	0.53	0.43	10	945	13	5	8	0	9
3NKB_B	-	0.41	0.42	0.42	8	716	11	4	7	0	11
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...	0.68	0.69	0.69	20	1504	9	4	5	0	9
3W3S_B	tRNA-Sec links to Rfam database...	0.94	0.91	0.97	30	1958	2	0	1	1	3
4AOB_A	SAM links to Rfam database...	0.60	0.59	0.63	17	1410	11	4	6	1	12
4ATO_G	-	0.38	0.43	0.38	3	212	5	5	0	0	4
4ENB_A	crcB links to Rfam database...	0.37	0.33	0.45	5	461	7	0	6	1	10
4ENC_A	crcB links to Rfam database...	0.36	0.33	0.42	5	484	8	0	7	1	10
4JRC_A	-	0.34	0.35	0.35	6	605	11	0	11	0	11

Total Scores
MCC	0.510
Average MCC ± 95% Confidence Intervals	0.505 ± 0.177
Sensitivity	0.455
Positive Predictive Value	0.592
Nr of predictions	14

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
3ADB_C	-	0.48	0.45	0.54	15	1791	13	1	12	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
3NKB_B	-	0.43	0.42	0.47	8	718	9	2	7	0	11
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.