CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	Afold		PPfold(seed)
MCC	0.492	>	0.127
Average MCC ± 95% Confidence Intervals	0.511 ± 0.238	>	0.078 ± 0.162
Sensitivity	0.439	>	0.031
Positive Predictive Value	0.559	>	0.538
Total TP	100	>	7
Total TN	35905	<	36071
Total FP	103	>	31
Total FP CONTRA	9	>	0
Total FP INCONS	70	>	6
Total FP COMP	24	<	25
Total FN	128	<	221
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	0.492
Average MCC ± 95% Confidence Intervals	0.511 ± 0.238
Sensitivity	0.439
Positive Predictive Value	0.559
Nr of predictions	7

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...	0.61	0.55	0.69	11	1524	6	0	5	1	9
3J3E_8	5_8S_rRNA links to Rfam database...	0.17	0.15	0.19	5	7477	31	2	19	10	28
3RKF_A	Purine links to Rfam database...	0.76	0.59	1.00	20	2191	0	0	0	0	14
3W3S_B	tRNA-Sec links to Rfam database...	0.50	0.45	0.56	18	4721	15	1	13	1	22
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	0.127
Average MCC ± 95% Confidence Intervals	0.078 ± 0.162
Sensitivity	0.031
Positive Predictive Value	0.538
Nr of predictions	7

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...	0.47	0.30	0.75	6	1532	2	0	2	0	14
3J3E_8	5_8S_rRNA links to Rfam database...	0.00	0.00	0.00	0	7503	6	0	0	6	33
3RKF_A	Purine links to Rfam database...	0.00	0.00	0.00	0	2211	0	0	0	0	34
3W3S_B	tRNA-Sec links to Rfam database...	0.00	0.00	0.00	0	4753	0	0	0	0	40
3ZEX_D	5S_rRNA links to Rfam database...	0.00	0.00	0.00	0	7021	0	0	0	0	49
4A1C_2	5_8S_rRNA links to Rfam database...	0.08	0.03	0.20	1	11776	23	0	4	19	32
4ENB_A	crcB links to Rfam database...	0.00	0.00	0.00	0	1275	0	0	0	0	19

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