CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	Afold		Multilign(20)
MCC	0.555	>	0.500
Average MCC ± 95% Confidence Intervals	0.603 ± 0.319	>	0.495 ± 0.410
Sensitivity	0.497	>	0.416
Positive Predictive Value	0.624	>	0.607
Total TP	98	>	82
Total TN	28272	<	28294
Total FP	71	>	57
Total FP CONTRA	7	>	6
Total FP INCONS	52	>	47
Total FP COMP	12	>	4
Total FN	99	<	115
P-value	0.0

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

Total Scores
MCC	0.555
Average MCC ± 95% Confidence Intervals	0.603 ± 0.319
Sensitivity	0.497
Positive Predictive Value	0.624
Nr of predictions	6

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	0.95	1.00	19	971	0	0	0	0	1
2XXA_G	Bacteria_small_SRP links to Rfam database...	0.34	0.31	0.39	13	5118	20	1	19	0	29
3RKF_A	Purine links to Rfam database...	0.76	0.59	1.00	20	2191	0	0	0	0	14
3ZEX_D	5S_rRNA links to Rfam database...	0.72	0.61	0.86	30	6986	5	0	5	0	19
4A1C_2	5_8S_rRNA links to Rfam database...	0.14	0.15	0.14	5	11745	43	5	26	12	28
4ENB_A	crcB links to Rfam database...	0.67	0.58	0.79	11	1261	3	1	2	0	8

Total Scores
MCC	0.500
Average MCC ± 95% Confidence Intervals	0.495 ± 0.410
Sensitivity	0.416
Positive Predictive Value	0.607
Nr of predictions	6

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	0.95	1.00	19	971	0	0	0	0	1
2XXA_G	Bacteria_small_SRP links to Rfam database...	0.00	0.00	0.00	0	5139	12	1	11	0	42
3RKF_A	Purine links to Rfam database...	0.77	0.62	0.95	21	2189	1	0	1	0	13
3ZEX_D	5S_rRNA links to Rfam database...	0.75	0.65	0.86	32	6984	5	1	4	0	17
4A1C_2	5_8S_rRNA links to Rfam database...	0.15	0.15	0.15	5	11747	33	3	26	4	28
4ENB_A	crcB links to Rfam database...	0.34	0.26	0.45	5	1264	6	1	5	0	14

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