CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	Afold		PPfold(seed)
MCC	0.529	>	0.171
Average MCC ± 95% Confidence Intervals	0.560 ± 0.305	>	0.098 ± 0.206
Sensitivity	0.560	>	0.056
Positive Predictive Value	0.511	<	0.538
Total TP	70	>	7
Total TN	10976	<	11100
Total FP	98	>	31
Total FP CONTRA	21	>	0
Total FP INCONS	46	>	6
Total FP COMP	31	>	25
Total FN	55	<	118
P-value	0.0

Comparison of performance of Afold and PPfold(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 Afold and PPfold(seed)).
Comparison of average Matthews Correlation Coefficients (MCCs) for Afold and PPfold(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 Afold and PPfold(seed)).

Total Scores
MCC	0.529
Average MCC ± 95% Confidence Intervals	0.560 ± 0.305
Sensitivity	0.560
Positive Predictive Value	0.511
Nr of predictions	6

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...	0.64	0.61	0.69	11	512	6	0	5	1	7
3J3E_8	5_8S_rRNA links to Rfam database...	0.26	0.33	0.21	5	2718	31	6	13	12	10
3RKF_A	Purine links to Rfam database...	0.91	0.83	1.00	20	846	0	0	0	0	4
3W3S_B	tRNA-Sec links to Rfam database...	0.55	0.55	0.56	18	1957	15	4	10	1	15
4A1C_2	5_8S_rRNA links to Rfam database...	0.19	0.25	0.15	5	4483	43	11	17	15	15
4ENB_A	crcB links to Rfam database...	0.81	0.73	0.92	11	460	3	0	1	2	4

Total Scores
MCC	0.171
Average MCC ± 95% Confidence Intervals	0.098 ± 0.206
Sensitivity	0.056
Positive Predictive Value	0.538
Nr of predictions	6

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...	0.49	0.33	0.75	6	520	2	0	2	0	12
3J3E_8	5_8S_rRNA links to Rfam database...	0.00	0.00	0.00	0	2742	6	0	0	6	15
3RKF_A	Purine links to Rfam database...	0.00	0.00	0.00	0	866	0	0	0	0	24
3W3S_B	tRNA-Sec links to Rfam database...	0.00	0.00	0.00	0	1989	0	0	0	0	33
4A1C_2	5_8S_rRNA links to Rfam database...	0.10	0.05	0.20	1	4511	23	0	4	19	19
4ENB_A	crcB links to Rfam database...	0.00	0.00	0.00	0	472	0	0	0	0	15

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