CompaRNA - on-line benchmarks of RNA structure prediction methods

FAQ

Metric	CentroidAlifold(seed)		Cylofold
MCC	0.792	>	0.677
Average MCC ± 95% Confidence Intervals	0.721 ± 0.161	>	0.691 ± 0.163
Sensitivity	0.656	>	0.646
Positive Predictive Value	0.962	>	0.718
Total TP	202	>	199
Total TN	20984	>	20917
Total FP	16	<	93
Total FP CONTRA	2	<	28
Total FP INCONS	6	<	50
Total FP COMP	8	<	15
Total FN	106	<	109
P-value	1.86109605532e-08

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

Total Scores
MCC	0.792
Average MCC ± 95% Confidence Intervals	0.721 ± 0.161
Sensitivity	0.656
Positive Predictive Value	0.962
Nr of predictions	12

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
3J20_0	tRNA links to Rfam database...	0.53	0.29	1.00	6	1213	0	0	0	0	15
3O58_3	5_8S_rRNA links to Rfam database...	0.68	0.50	0.92	11	4752	2	1	0	1	11
3PDR_A	ykoK links to Rfam database...	0.93	0.88	0.98	44	4795	3	0	1	2	6
3RKF_A	Purine links to Rfam database...	0.91	0.83	1.00	20	846	0	0	0	0	4
3SD1_A	THF links to Rfam database...	0.85	0.76	0.96	22	1510	1	0	1	0	7
3W3S_B	tRNA-Sec links to Rfam database...	0.80	0.70	0.92	23	1964	4	0	2	2	10
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
4FRG_B	AdoCbl-variant links to Rfam database...	0.81	0.71	0.94	17	1184	2	0	1	1	7
4FRN_A	AdoCbl-variant links to Rfam database...	0.80	0.71	0.91	20	1826	2	1	1	0	8

Total Scores
MCC	0.677
Average MCC ± 95% Confidence Intervals	0.691 ± 0.163
Sensitivity	0.646
Positive Predictive Value	0.718
Nr of predictions	12

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...	0.64	0.61	0.69	11	512	5	1	4	0	7
3J20_0	tRNA links to Rfam database...	0.74	0.76	0.73	16	1197	7	3	3	1	5
3O58_3	5_8S_rRNA links to Rfam database...	0.42	0.50	0.35	11	4733	30	9	11	10	11
3PDR_A	ykoK links to Rfam database...	0.86	0.78	0.95	39	4799	4	1	1	2	11
3RKF_A	Purine links to Rfam database...	0.91	0.83	1.00	20	846	0	0	0	0	4
3SD1_A	THF links to Rfam database...	0.71	0.69	0.74	20	1506	7	2	5	0	9
3W3S_B	tRNA-Sec links to Rfam database...	0.48	0.45	0.52	15	1960	15	1	13	1	18
4AOB_A	SAM links to Rfam database...	0.42	0.38	0.48	11	1414	13	3	9	1	18
4ENB_A	crcB links to Rfam database...	1.00	1.00	1.00	15	457	0	0	0	0	0
4ENC_A	crcB links to Rfam database...	0.97	1.00	0.94	15	480	1	1	0	0	0
4FRG_B	AdoCbl-variant links to Rfam database...	0.93	0.88	1.00	21	1181	0	0	0	0	3
4FRN_A	AdoCbl-variant links to Rfam database...	0.23	0.18	0.31	5	1832	11	7	4	0	23

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