CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	CRWrnafold		RDfolder
MCC	0.513	>	0.230
Average MCC ± 95% Confidence Intervals	0.437 ± 0.236	>	0.187 ± 0.133
Sensitivity	0.436	>	0.165
Positive Predictive Value	0.613	>	0.336
Total TP	103	>	39
Total TN	20856	<	20908
Total FP	68	<	80
Total FP CONTRA	10	>	7
Total FP INCONS	55	<	70
Total FP COMP	3	=	3
Total FN	133	<	197
P-value	7.60513176667e-09

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

Total Scores
MCC	0.513
Average MCC ± 95% Confidence Intervals	0.437 ± 0.236
Sensitivity	0.436
Positive Predictive Value	0.613
Nr of predictions	10

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	1525	15	2	13	0	20
3AMU_B	tRNA links to Rfam database...	0.67	0.59	0.76	16	2982	7	0	5	2	11
3J0L_7	-	-0.01	0.00	0.00	0	1212	13	0	13	0	17
3J0L_a	-	0.39	0.31	0.50	5	1118	5	1	4	0	11
3J0L_g	-	-0.01	0.00	0.00	0	461	4	1	3	0	4
3J16_L	tRNA links to Rfam database...	0.84	0.70	1.00	21	2754	0	0	0	0	9
3SD1_A	THF links to Rfam database...	0.52	0.45	0.61	19	3885	12	2	10	0	23
4AOB_A	SAM links to Rfam database...	0.59	0.48	0.74	20	4344	8	2	5	1	22
4ENB_A	crcB links to Rfam database...	0.70	0.58	0.85	11	1262	2	1	1	0	8
4ENC_A	crcB links to Rfam database...	0.70	0.58	0.85	11	1313	2	1	1	0	8

Total Scores
MCC	0.230
Average MCC ± 95% Confidence Intervals	0.187 ± 0.133
Sensitivity	0.165
Positive Predictive Value	0.336
Nr of predictions	10

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
3AMU_B	tRNA links to Rfam database...	0.18	0.15	0.22	4	2985	16	2	12	2	23
3J0L_7	-	-0.01	0.00	0.00	0	1220	5	0	5	0	17
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
3J16_L	tRNA links to Rfam database...	0.22	0.17	0.31	5	2759	11	0	11	0	25
3SD1_A	THF links to Rfam database...	0.30	0.17	0.54	7	3903	6	0	6	0	35
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.