CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	Multilign(seed)		RSpredict(seed)
MCC	0.679	>	0.341
Average MCC ± 95% Confidence Intervals	0.634 ± 0.237	>	0.264 ± 0.207
Sensitivity	0.629	>	0.209
Positive Predictive Value	0.742	>	0.574
Total TP	175	>	58
Total TN	19198	<	19333
Total FP	64	>	45
Total FP CONTRA	21	>	4
Total FP INCONS	40	>	39
Total FP COMP	3	>	2
Total FN	103	<	220
P-value	1.29018360962e-08

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

Total Scores
MCC	0.679
Average MCC ± 95% Confidence Intervals	0.634 ± 0.237
Sensitivity	0.629
Positive Predictive Value	0.742
Nr of predictions	11

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	0.94	1.00	17	340	0	0	0	0	1
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
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...	0.66	0.66	0.68	19	1505	9	4	5	0	10
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	0.341
Average MCC ± 95% Confidence Intervals	0.264 ± 0.207
Sensitivity	0.209
Positive Predictive Value	0.574
Nr of predictions	11

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...	0.55	0.50	0.64	9	343	6	0	5	1	9
2LC8_A	GP_knot1 links to Rfam database...	-0.03	0.00	0.00	0	515	13	0	13	0	18
3J3E_8	5_8S_rRNA links to Rfam database...	0.00	0.00	0.00	0	2742	0	0	0	0	15
3RKF_A	Purine links to Rfam database...	0.84	0.75	0.95	18	847	1	1	0	0	6
3SD1_A	THF links to Rfam database...	0.00	0.00	0.00	0	1533	0	0	0	0	29
3W1K_J	tRNA-Sec links to Rfam database...	0.57	0.35	0.92	11	1666	1	0	1	0	20
3W3S_B	tRNA-Sec links to Rfam database...	0.45	0.36	0.57	12	1968	10	1	8	1	21
3ZEX_C	5_8S_rRNA links to Rfam database...	0.13	0.07	0.25	2	5366	6	2	4	0	27
4AOB_A	SAM links to Rfam database...	0.42	0.21	0.86	6	1430	1	0	1	0	23
4FRN_A	AdoCbl-variant links to Rfam database...	0.00	0.00	0.00	0	1845	3	0	3	0	28
4JF2_A	preQ1-II links to Rfam database...	-0.01	0.00	0.00	0	1078	4	0	4	0	24

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