CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	CRWrnafold		MCFold
MCC	0.459	>	0.434
Average MCC ± 95% Confidence Intervals	0.482 ± 0.305	>	0.436 ± 0.229
Sensitivity	0.477	>	0.469
Positive Predictive Value	0.456	>	0.418
Total TP	62	>	61
Total TN	9096	>	9086
Total FP	95	<	110
Total FP CONTRA	23	>	15
Total FP INCONS	51	<	70
Total FP COMP	21	<	25
Total FN	68	<	69
P-value	0.0

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

Total Scores
MCC	0.459
Average MCC ± 95% Confidence Intervals	0.482 ± 0.305
Sensitivity	0.477
Positive Predictive Value	0.456
Nr of predictions	7

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
3J0L_a	-	0.39	0.36	0.44	4	402	6	3	2	1	7
3SD1_A	THF links to Rfam database...	0.63	0.66	0.61	19	1502	12	6	6	0	10
3U4M_B	-	0.49	0.55	0.46	12	1250	14	3	11	0	10
4A1C_2	5_8S_rRNA links to Rfam database...	0.19	0.25	0.15	5	4483	44	8	20	16	15
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

Total Scores
MCC	0.434
Average MCC ± 95% Confidence Intervals	0.436 ± 0.229
Sensitivity	0.469
Positive Predictive Value	0.418
Nr of predictions	7

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...	0.44	0.44	0.47	8	511	10	0	9	1	10
3J0L_a	-	0.14	0.18	0.15	2	398	13	1	10	2	9
3SD1_A	THF links to Rfam database...	0.43	0.45	0.43	13	1503	17	1	16	0	16
3U4M_B	-	0.74	0.77	0.71	17	1252	10	1	6	3	5
4A1C_2	5_8S_rRNA links to Rfam database...	0.18	0.25	0.14	5	4480	45	12	19	14	15
4ENB_A	crcB links to Rfam database...	0.78	0.73	0.85	11	459	4	0	2	2	4
4ENC_A	crcB links to Rfam database...	0.34	0.33	0.38	5	483	11	0	8	3	10

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