CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	TurboFold(seed)		PPfold(seed)
MCC	0.621	>	0.139
Average MCC ± 95% Confidence Intervals	0.602 ± 0.280	>	0.073 ± 0.143
Sensitivity	0.594	>	0.037
Positive Predictive Value	0.661	>	0.538
Total TP	111	>	7
Total TN	12443	<	12598
Total FP	72	>	25
Total FP CONTRA	17	>	0
Total FP INCONS	40	>	6
Total FP COMP	15	<	19
Total FN	76	<	180
P-value	0.0

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

Total Scores
MCC	0.621
Average MCC ± 95% Confidence Intervals	0.602 ± 0.280
Sensitivity	0.594
Positive Predictive Value	0.661
Nr of predictions	8

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...	-0.03	0.00	0.00	0	513	15	3	12	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...	0.71	0.69	0.74	20	1506	7	2	5	0	9
4A1C_2	5_8S_rRNA links to Rfam database...	0.20	0.25	0.17	5	4486	37	9	16	12	15
4A1C_3	5S_rRNA links to Rfam database...	0.86	0.84	0.89	31	2728	6	0	4	2	6
4AOB_A	SAM links to Rfam database...	0.67	0.59	0.77	17	1415	6	2	3	1	12
4ENB_A	crcB links to Rfam database...	0.77	0.60	1.00	9	463	0	0	0	0	6
4ENC_A	crcB links to Rfam database...	0.73	0.60	0.90	9	486	1	1	0	0	6

Total Scores
MCC	0.139
Average MCC ± 95% Confidence Intervals	0.073 ± 0.143
Sensitivity	0.037
Positive Predictive Value	0.538
Nr of predictions	8

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
3RKF_A	Purine links to Rfam database...	0.00	0.00	0.00	0	866	0	0	0	0	24
3SD1_A	THF links to Rfam database...	0.00	0.00	0.00	0	1533	0	0	0	0	29
4A1C_2	5_8S_rRNA links to Rfam database...	0.10	0.05	0.20	1	4511	23	0	4	19	19
4A1C_3	5S_rRNA links to Rfam database...	0.00	0.00	0.00	0	2763	0	0	0	0	37
4AOB_A	SAM links to Rfam database...	0.00	0.00	0.00	0	1437	0	0	0	0	29
4ENB_A	crcB links to Rfam database...	0.00	0.00	0.00	0	472	0	0	0	0	15
4ENC_A	crcB links to Rfam database...	0.00	0.00	0.00	0	496	0	0	0	0	15

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