CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	Multilign(seed)		RNAalifold(seed)
MCC	0.658	>	0.641
Average MCC ± 95% Confidence Intervals	0.601 ± 0.253	>	0.564 ± 0.229
Sensitivity	0.608	>	0.485
Positive Predictive Value	0.721	<	0.857
Total TP	158	>	126
Total TN	18858	<	18930
Total FP	64	>	27
Total FP CONTRA	21	>	5
Total FP INCONS	40	>	16
Total FP COMP	3	<	6
Total FN	102	<	134
P-value	0.00176439510334

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

Total Scores
MCC	0.658
Average MCC ± 95% Confidence Intervals	0.601 ± 0.253
Sensitivity	0.608
Positive Predictive Value	0.721
Nr of predictions	10

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
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	0.641
Average MCC ± 95% Confidence Intervals	0.564 ± 0.229
Sensitivity	0.485
Positive Predictive Value	0.857
Nr of predictions	10

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	0	12	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...	0.74	0.67	0.84	16	847	3	1	2	0	8
3SD1_A	THF links to Rfam database...	0.70	0.59	0.85	17	1513	3	2	1	0	12
3W1K_J	tRNA-Sec links to Rfam database...	0.78	0.61	1.00	19	1659	0	0	0	0	12
3W3S_B	tRNA-Sec links to Rfam database...	0.71	0.52	1.00	17	1972	2	0	0	2	16
3ZEX_C	5_8S_rRNA links to Rfam database...	0.49	0.24	1.00	7	5367	2	0	0	2	22
4AOB_A	SAM links to Rfam database...	0.85	0.72	1.00	21	1416	2	0	0	2	8
4FRN_A	AdoCbl-variant links to Rfam database...	0.78	0.68	0.90	19	1827	2	1	1	0	9
4JF2_A	preQ1-II links to Rfam database...	0.61	0.42	0.91	10	1071	1	1	0	0	14

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