CompaRNA - on-line benchmarks of RNA structure prediction methods

FAQ

Metric	CentroidHomfold‑LAST		Multilign(seed)
MCC	0.549	>	0.534
Average MCC ± 95% Confidence Intervals	0.512 ± 0.282	>	0.487 ± 0.272
Sensitivity	0.435	>	0.414
Positive Predictive Value	0.699	>	0.697
Total TP	121	>	115
Total TN	32122	<	32130
Total FP	58	>	52
Total FP CONTRA	4	<	8
Total FP INCONS	48	>	42
Total FP COMP	6	>	2
Total FN	157	<	163
P-value	0.0

Comparison of performance of CentroidHomfold-LAST and Multilign(seed). 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 CentroidHomfold‑LAST and Multilign(seed)).
Comparison of average Matthews Correlation Coefficients (MCCs) for CentroidHomfold-LAST and Multilign(seed). 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 CentroidHomfold‑LAST and Multilign(seed)).

Total Scores
MCC	0.549
Average MCC ± 95% Confidence Intervals	0.512 ± 0.282
Sensitivity	0.435
Positive Predictive Value	0.699
Nr of predictions	8

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...	-0.01	0.00	0.00	0	1529	11	0	11	0	20
3J3E_8	5_8S_rRNA links to Rfam database...	0.05	0.03	0.08	1	7490	16	1	11	4	32
3RKF_A	Purine links to Rfam database...	0.72	0.53	1.00	18	2193	0	0	0	0	16
3SD1_A	THF links to Rfam database...	0.64	0.45	0.90	19	3895	2	0	2	0	23
3W3S_B	tRNA-Sec links to Rfam database...	0.85	0.73	1.00	29	4724	1	0	0	1	11
4AOB_A	SAM links to Rfam database...	0.71	0.50	1.00	21	4350	1	0	0	1	21
4FRN_A	AdoCbl-variant links to Rfam database...	0.36	0.39	0.34	14	5110	27	3	24	0	22
4JF2_A	preQ1-II links to Rfam database...	0.78	0.61	1.00	19	2831	0	0	0	0	12

Total Scores
MCC	0.534
Average MCC ± 95% Confidence Intervals	0.487 ± 0.272
Sensitivity	0.414
Positive Predictive Value	0.697
Nr of predictions	8

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...	-0.01	0.00	0.00	0	1528	12	1	11	0	20
3J3E_8	5_8S_rRNA links to Rfam database...	0.13	0.09	0.19	3	7487	13	5	8	0	30
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...	0.55	0.45	0.68	19	3888	9	1	8	0	23
3W3S_B	tRNA-Sec links to Rfam database...	0.84	0.73	0.97	29	4723	2	0	1	1	11
4AOB_A	SAM links to Rfam database...	0.61	0.45	0.83	19	4348	5	0	4	1	23
4FRN_A	AdoCbl-variant links to Rfam database...	0.24	0.17	0.35	6	5134	11	1	10	0	30
4JF2_A	preQ1-II links to Rfam database...	0.78	0.61	1.00	19	2831	0	0	0	0	12

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