CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	Multilign(20)		RDfolder
MCC	0.716	>	0.584
Average MCC ± 95% Confidence Intervals	0.712 ± 0.156	>	0.582 ± 0.242
Sensitivity	0.694	>	0.518
Positive Predictive Value	0.752	>	0.677
Total TP	118	>	88
Total TN	7380	<	7407
Total FP	46	<	47
Total FP CONTRA	10	>	9
Total FP INCONS	29	<	33
Total FP COMP	7	>	5
Total FN	52	<	82
P-value	0.0

Comparison of performance of Multilign(20) and RDfolder. 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(20) and RDfolder).
Comparison of average Matthews Correlation Coefficients (MCCs) for Multilign(20) and RDfolder. 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(20) and RDfolder).

Total Scores
MCC	0.716
Average MCC ± 95% Confidence Intervals	0.712 ± 0.156
Sensitivity	0.694
Positive Predictive Value	0.752
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...	1.00	1.00	1.00	18	339	1	0	0	1	0
3AMU_B	tRNA links to Rfam database...	0.71	0.74	0.70	14	1137	9	0	6	3	5
3J20_0	tRNA links to Rfam database...	0.68	0.71	0.65	15	1196	9	2	6	1	6
3RKF_A	Purine links to Rfam database...	0.91	0.88	0.95	21	844	1	0	1	0	3
3SD1_A	THF links to Rfam database...	0.68	0.69	0.69	20	1504	9	4	5	0	9
4AOB_A	SAM links to Rfam database...	0.59	0.55	0.64	16	1412	10	3	6	1	13
4ENB_A	crcB links to Rfam database...	0.39	0.33	0.50	5	462	6	0	5	1	10
4ENC_A	crcB links to Rfam database...	0.73	0.60	0.90	9	486	1	1	0	0	6

Total Scores
MCC	0.584
Average MCC ± 95% Confidence Intervals	0.582 ± 0.242
Sensitivity	0.518
Positive Predictive Value	0.677
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...	1.00	1.00	1.00	18	339	1	0	0	1	0
3AMU_B	tRNA links to Rfam database...	0.20	0.21	0.22	4	1139	16	4	10	2	15
3J20_0	tRNA links to Rfam database...	0.82	0.76	0.89	16	1201	3	1	1	1	5
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...	0.35	0.24	0.54	7	1520	6	1	5	0	22
4AOB_A	SAM links to Rfam database...	0.42	0.38	0.48	11	1414	13	3	9	1	18
4ENB_A	crcB links to Rfam database...	0.48	0.40	0.60	6	462	4	0	4	0	9
4ENC_A	crcB links to Rfam database...	0.48	0.40	0.60	6	486	4	0	4	0	9

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