CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	Murlet(20)		Cylofold
MCC	0.685	>	0.661
Average MCC ± 95% Confidence Intervals	0.659 ± 0.110	<	0.682 ± 0.122
Sensitivity	0.528	<	0.553
Positive Predictive Value	0.893	>	0.796
Total TP	216	<	226
Total TN	58156	>	58114
Total FP	33	<	73
Total FP CONTRA	3	<	11
Total FP INCONS	23	<	47
Total FP COMP	7	<	15
Total FN	193	>	183
P-value	2.35850794473e-08

Comparison of performance of Murlet(20) and Cylofold. 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 Murlet(20) and Cylofold).
Comparison of average Matthews Correlation Coefficients (MCCs) for Murlet(20) and Cylofold. 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 Murlet(20) and Cylofold).

Total Scores
MCC	0.685
Average MCC ± 95% Confidence Intervals	0.659 ± 0.110
Sensitivity	0.528
Positive Predictive Value	0.893
Nr of predictions	11

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2XQD_Y	tRNA links to Rfam database...	0.80	0.70	0.90	19	2829	2	0	2	0	8
3AMU_B	tRNA links to Rfam database...	0.77	0.67	0.90	18	2983	3	0	2	1	9
3IZF_C	5S_rRNA links to Rfam database...	0.71	0.56	0.91	30	6870	4	0	3	1	24
3O58_2	5S_rRNA links to Rfam database...	0.89	0.82	0.97	31	7228	2	0	1	1	7
3O58_3	5_8S_rRNA links to Rfam database...	0.33	0.23	0.47	8	12386	12	2	7	3	27
3PDR_A	ykoK links to Rfam database...	0.70	0.53	0.93	38	12839	3	0	3	0	34
3RKF_A	Purine links to Rfam database...	0.68	0.47	1.00	16	2195	0	0	0	0	18
3SD1_A	THF links to Rfam database...	0.68	0.57	0.83	24	3887	5	1	4	0	18
4AOB_A	SAM links to Rfam database...	0.72	0.55	0.96	23	4347	2	0	1	1	19
4ENB_A	crcB links to Rfam database...	0.46	0.21	1.00	4	1271	0	0	0	0	15
4ENC_A	crcB links to Rfam database...	0.51	0.26	1.00	5	1321	0	0	0	0	14

Total Scores
MCC	0.661
Average MCC ± 95% Confidence Intervals	0.682 ± 0.122
Sensitivity	0.553
Positive Predictive Value	0.796
Nr of predictions	11

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2XQD_Y	tRNA links to Rfam database...	0.81	0.78	0.84	21	2825	4	4	0	0	6
3AMU_B	tRNA links to Rfam database...	0.67	0.59	0.76	16	2982	7	0	5	2	11
3IZF_C	5S_rRNA links to Rfam database...	0.68	0.56	0.83	30	6867	6	0	6	0	24
3O58_2	5S_rRNA links to Rfam database...	0.80	0.68	0.93	26	7232	3	0	2	1	12
3O58_3	5_8S_rRNA links to Rfam database...	0.36	0.34	0.38	12	12371	29	5	15	9	23
3PDR_A	ykoK links to Rfam database...	0.72	0.54	0.95	39	12839	4	0	2	2	33
3RKF_A	Purine links to Rfam database...	0.76	0.59	1.00	20	2191	0	0	0	0	14
3SD1_A	THF links to Rfam database...	0.62	0.50	0.78	21	3889	6	0	6	0	21
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...	0.89	0.79	1.00	15	1260	0	0	0	0	4
4ENC_A	crcB links to Rfam database...	0.86	0.79	0.94	15	1310	1	1	0	0	4

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