CompaRNA - on-line benchmarks of RNA structure prediction methods

FAQ

Metric	Multilign(seed)		RNASLOpt
MCC	0.628	>	0.536
Average MCC ± 95% Confidence Intervals	0.554 ± 0.317	>	0.503 ± 0.303
Sensitivity	0.575	>	0.507
Positive Predictive Value	0.696	>	0.577
Total TP	119	>	105
Total TN	16507	>	16496
Total FP	55	<	104
Total FP CONTRA	17	<	24
Total FP INCONS	35	<	53
Total FP COMP	3	<	27
Total FN	88	<	102
P-value	0.0

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

Total Scores
MCC	0.628
Average MCC ± 95% Confidence Intervals	0.554 ± 0.317
Sensitivity	0.575
Positive Predictive Value	0.696
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...	-0.03	0.00	0.00	0	516	12	2	10	0	18
3J3E_8	5_8S_rRNA links to Rfam database...	0.19	0.20	0.19	3	2726	13	8	5	0	12
3W1K_J	tRNA-Sec links to Rfam database...	0.97	0.97	0.97	30	1647	1	1	0	0	1
3W3S_B	tRNA-Sec links to Rfam database...	0.92	0.88	0.97	29	1959	2	0	1	1	4
3ZEX_C	5_8S_rRNA links to Rfam database...	0.50	0.45	0.57	13	5351	11	3	7	1	16
4AOB_A	SAM links to Rfam database...	0.73	0.66	0.83	19	1414	5	1	3	1	10
4FRN_A	AdoCbl-variant links to Rfam database...	0.27	0.21	0.35	6	1831	11	2	9	0	22
4JF2_A	preQ1-II links to Rfam database...	0.89	0.79	1.00	19	1063	0	0	0	0	5

Total Scores
MCC	0.536
Average MCC ± 95% Confidence Intervals	0.503 ± 0.303
Sensitivity	0.507
Positive Predictive Value	0.577
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...	0.48	0.39	0.64	7	517	4	0	4	0	11
3J3E_8	5_8S_rRNA links to Rfam database...	-0.01	0.00	0.00	0	2724	30	6	12	12	15
3W1K_J	tRNA-Sec links to Rfam database...	0.93	0.90	0.97	28	1649	1	1	0	0	3
3W3S_B	tRNA-Sec links to Rfam database...	0.90	0.85	0.97	28	1960	2	0	1	1	5
3ZEX_C	5_8S_rRNA links to Rfam database...	0.32	0.34	0.31	10	5342	36	8	14	14	19
4AOB_A	SAM links to Rfam database...	0.31	0.28	0.38	8	1416	13	3	10	0	21
4FRN_A	AdoCbl-variant links to Rfam database...	0.19	0.18	0.22	5	1825	18	6	12	0	23
4JF2_A	preQ1-II links to Rfam database...	0.89	0.79	1.00	19	1063	0	0	0	0	5

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