CompaRNA - on-line benchmarks of RNA structure prediction methods

FAQ

Metric	Multilign(seed)		MCFold
MCC	0.481	>	0.396
Average MCC ± 95% Confidence Intervals	0.471 ± 0.283	>	0.445 ± 0.256
Sensitivity	0.366	<	0.392
Positive Predictive Value	0.641	>	0.409
Total TP	98	<	105
Total TN	38204	>	38100
Total FP	55	<	173
Total FP CONTRA	11	>	8
Total FP INCONS	44	<	144
Total FP COMP	0	<	21
Total FN	170	>	163
P-value	0.0

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

Total Scores
MCC	0.481
Average MCC ± 95% Confidence Intervals	0.471 ± 0.283
Sensitivity	0.366
Positive Predictive Value	0.641
Nr of predictions	8

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2L94_A	HIV_FE links to Rfam database...	0.92	0.85	1.00	17	973	0	0	0	0	3
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
3ZEX_C	5_8S_rRNA links to Rfam database...	0.39	0.27	0.58	14	14172	10	3	7	0	38
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

Total Scores
MCC	0.396
Average MCC ± 95% Confidence Intervals	0.445 ± 0.256
Sensitivity	0.392
Positive Predictive Value	0.409
Nr of predictions	8

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2L94_A	HIV_FE links to Rfam database...	0.97	0.95	1.00	19	971	0	0	0	0	1
2LC8_A	GP_knot1 links to Rfam database...	0.41	0.45	0.39	9	1517	16	0	14	2	11
3J3E_8	5_8S_rRNA links to Rfam database...	0.12	0.12	0.12	4	7470	46	3	26	17	29
3RKF_A	Purine links to Rfam database...	0.70	0.65	0.76	22	2182	7	1	6	0	12
3SD1_A	THF links to Rfam database...	0.33	0.33	0.35	14	3876	26	0	26	0	28
3ZEX_C	5_8S_rRNA links to Rfam database...	0.24	0.21	0.28	11	14156	29	3	26	0	41
4FRN_A	AdoCbl-variant links to Rfam database...	0.12	0.14	0.12	5	5110	38	1	35	2	31
4JF2_A	preQ1-II links to Rfam database...	0.66	0.68	0.66	21	2818	11	0	11	0	10

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