CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	Contrafold		Multilign(seed)
MCC	0.699	>	0.649
Average MCC ± 95% Confidence Intervals	0.695 ± 0.193	>	0.617 ± 0.295
Sensitivity	0.678	>	0.591
Positive Predictive Value	0.731	>	0.724
Total TP	141	>	123
Total TN	13739	<	13762
Total FP	61	>	50
Total FP CONTRA	18	>	12
Total FP INCONS	34	<	35
Total FP COMP	9	>	3
Total FN	67	<	85
P-value	0.0

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

Total Scores
MCC	0.699
Average MCC ± 95% Confidence Intervals	0.695 ± 0.193
Sensitivity	0.678
Positive Predictive Value	0.731
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...	0.94	0.94	0.94	17	339	2	0	1	1	1
2LC8_A	GP_knot1 links to Rfam database...	0.46	0.39	0.58	7	516	5	3	2	0	11
3RKF_A	Purine links to Rfam database...	0.87	0.83	0.91	20	844	2	2	0	0	4
3SD1_A	THF links to Rfam database...	0.68	0.69	0.69	20	1504	9	5	4	0	9
3W3S_B	tRNA-Sec links to Rfam database...	0.98	0.97	1.00	32	1957	1	0	0	1	1
3ZEX_C	5_8S_rRNA links to Rfam database...	0.35	0.34	0.37	10	5347	23	4	13	6	19
4AOB_A	SAM links to Rfam database...	0.53	0.52	0.56	15	1410	13	3	9	1	14
4FRN_A	AdoCbl-variant links to Rfam database...	0.74	0.71	0.77	20	1822	6	1	5	0	8

Total Scores
MCC	0.649
Average MCC ± 95% Confidence Intervals	0.617 ± 0.295
Sensitivity	0.591
Positive Predictive Value	0.724
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	0.94	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
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
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

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