CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	CentroidAlifold(seed)		CRWrnafold
MCC	0.678	>	0.647
Average MCC ± 95% Confidence Intervals	0.609 ± 0.202	<	0.646 ± 0.263
Sensitivity	0.473	<	0.655
Positive Predictive Value	0.980	>	0.649
Total TP	96	<	133
Total TN	13963	>	13856
Total FP	7	<	98
Total FP CONTRA	1	<	21
Total FP INCONS	1	<	51
Total FP COMP	5	<	26
Total FN	107	>	70
P-value	0.0

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

Total Scores
MCC	0.678
Average MCC ± 95% Confidence Intervals	0.609 ± 0.202
Sensitivity	0.473
Positive Predictive Value	0.980
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...	0.00	0.00	0.00	0	528	0	0	0	0	18
3AMU_B	tRNA links to Rfam database...	0.51	0.26	1.00	5	1152	1	0	0	1	14
3J16_L	tRNA links to Rfam database...	0.53	0.29	1.00	6	1153	0	0	0	0	15
3SD1_A	THF links to Rfam database...	0.85	0.76	0.96	22	1510	1	0	1	0	7
4A1C_3	5S_rRNA links to Rfam database...	0.66	0.43	1.00	16	2747	0	0	0	0	21
4A1C_2	5_8S_rRNA links to Rfam database...	0.60	0.40	0.89	8	4507	3	1	0	2	12
4AOB_A	SAM links to Rfam database...	0.89	0.79	1.00	23	1414	2	0	0	2	6
4ENB_A	crcB links to Rfam database...	0.72	0.53	1.00	8	464	0	0	0	0	7
4ENC_A	crcB links to Rfam database...	0.73	0.53	1.00	8	488	0	0	0	0	7

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.