CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	MXScarna(seed)		CRWrnafold
MCC	0.705	>	0.647
Average MCC ± 95% Confidence Intervals	0.639 ± 0.248	<	0.646 ± 0.263
Sensitivity	0.660	>	0.655
Positive Predictive Value	0.761	>	0.649
Total TP	134	>	133
Total TN	13885	>	13856
Total FP	65	<	98
Total FP CONTRA	11	<	21
Total FP INCONS	31	<	51
Total FP COMP	23	<	26
Total FN	69	<	70
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	0.705
Average MCC ± 95% Confidence Intervals	0.639 ± 0.248
Sensitivity	0.660
Positive Predictive Value	0.761
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...	-0.03	0.00	0.00	0	518	12	0	10	2	18
3AMU_B	tRNA links to Rfam database...	0.97	0.95	1.00	18	1139	2	0	0	2	1
3J16_L	tRNA links to Rfam database...	0.98	0.95	1.00	20	1139	0	0	0	0	1
3SD1_A	THF links to Rfam database...	0.74	0.76	0.73	22	1503	9	4	4	1	7
4A1C_3	5S_rRNA links to Rfam database...	0.92	0.92	0.92	34	2726	6	0	3	3	3
4A1C_2	5_8S_rRNA links to Rfam database...	0.45	0.40	0.50	8	4500	20	4	4	12	12
4AOB_A	SAM links to Rfam database...	0.71	0.69	0.74	20	1410	10	2	5	3	9
4ENB_A	crcB links to Rfam database...	0.54	0.40	0.75	6	464	2	0	2	0	9
4ENC_A	crcB links to Rfam database...	0.48	0.40	0.60	6	486	4	1	3	0	9

Total Scores
MCC	0.647
Average MCC ± 95% Confidence Intervals	0.646 ± 0.263
Sensitivity	0.655
Positive Predictive Value	0.649
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...	-0.03	0.00	0.00	0	513	15	3	12	0	18
3AMU_B	tRNA links to Rfam database...	0.77	0.79	0.75	15	1137	8	0	5	3	4
3J16_L	tRNA links to Rfam database...	1.00	1.00	1.00	21	1138	0	0	0	0	0
3SD1_A	THF links to Rfam database...	0.63	0.66	0.61	19	1502	12	6	6	0	10
4A1C_3	5S_rRNA links to Rfam database...	0.85	0.84	0.86	31	2727	7	0	5	2	6
4A1C_2	5_8S_rRNA links to Rfam database...	0.19	0.25	0.15	5	4483	44	8	20	16	15
4AOB_A	SAM links to Rfam database...	0.71	0.69	0.74	20	1410	8	4	3	1	9
4ENB_A	crcB links to Rfam database...	0.85	0.73	1.00	11	461	2	0	0	2	4
4ENC_A	crcB links to Rfam database...	0.85	0.73	1.00	11	485	2	0	0	2	4

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