CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	MXScarna(seed)		CRWrnafold
MCC	0.610	>	0.536
Average MCC ± 95% Confidence Intervals	0.549 ± 0.208	>	0.538 ± 0.219
Sensitivity	0.490	>	0.472
Positive Predictive Value	0.765	>	0.616
Total TP	140	>	135
Total TN	36944	>	36908
Total FP	59	<	96
Total FP CONTRA	4	<	12
Total FP INCONS	39	<	72
Total FP COMP	16	>	12
Total FN	146	<	151
P-value	0.0

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

Total Scores
MCC	0.610
Average MCC ± 95% Confidence Intervals	0.549 ± 0.208
Sensitivity	0.490
Positive Predictive Value	0.765
Nr of predictions	9

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	1530	12	0	10	2	20
3AMU_B	tRNA links to Rfam database...	0.84	0.70	1.00	19	2984	1	0	0	1	8
3J16_L	tRNA links to Rfam database...	0.82	0.67	1.00	20	2755	0	0	0	0	10
3SD1_A	THF links to Rfam database...	0.63	0.55	0.74	23	3885	8	1	7	0	19
4A1C_3	5S_rRNA links to Rfam database...	0.75	0.65	0.88	35	7100	5	1	4	0	19
4A1C_2	5_8S_rRNA links to Rfam database...	0.35	0.24	0.50	8	11765	20	1	7	12	25
4AOB_A	SAM links to Rfam database...	0.66	0.55	0.79	23	4342	7	0	6	1	19
4ENB_A	crcB links to Rfam database...	0.48	0.32	0.75	6	1267	2	0	2	0	13
4ENC_A	crcB links to Rfam database...	0.43	0.32	0.60	6	1316	4	1	3	0	13

Total Scores
MCC	0.536
Average MCC ± 95% Confidence Intervals	0.538 ± 0.219
Sensitivity	0.472
Positive Predictive Value	0.616
Nr of predictions	9

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
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
4A1C_3	5S_rRNA links to Rfam database...	0.70	0.59	0.84	32	7102	6	0	6	0	22
4A1C_2	5_8S_rRNA links to Rfam database...	0.13	0.15	0.13	5	11741	44	4	31	9	28
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

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