CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	CentroidAlifold(20)		PPfold(seed)
MCC	0.825	>	0.031
Average MCC ± 95% Confidence Intervals	0.789 ± 0.174	>	0.012 ± 0.029
Sensitivity	0.729	>	0.005
Positive Predictive Value	0.938	>	0.200
Total TP	137	>	1
Total TN	13094	<	13235
Total FP	17	<	23
Total FP CONTRA	3	>	0
Total FP INCONS	6	>	4
Total FP COMP	8	<	19
Total FN	51	<	187
P-value	0.0

Comparison of performance of CentroidAlifold(20) 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 CentroidAlifold(20) and PPfold(seed)).
Comparison of average Matthews Correlation Coefficients (MCCs) for CentroidAlifold(20) 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 CentroidAlifold(20) and PPfold(seed)).

Total Scores
MCC	0.825
Average MCC ± 95% Confidence Intervals	0.789 ± 0.174
Sensitivity	0.729
Positive Predictive Value	0.938
Nr of predictions	8

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
3AMU_B	tRNA links to Rfam database...	1.00	1.00	1.00	19	1138	2	0	0	2	0
3RKF_A	Purine links to Rfam database...	0.86	0.75	1.00	18	848	0	0	0	0	6
3SD1_A	THF links to Rfam database...	0.85	0.76	0.96	22	1510	1	0	1	0	7
4A1C_2	5_8S_rRNA links to Rfam database...	0.33	0.25	0.45	5	4505	8	3	3	2	15
4A1C_3	5S_rRNA links to Rfam database...	0.93	0.92	0.94	34	2727	4	0	2	2	3
4AOB_A	SAM links to Rfam database...	0.89	0.79	1.00	23	1414	2	0	0	2	6
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...	0.68	0.47	1.00	7	489	0	0	0	0	8

Total Scores
MCC	0.031
Average MCC ± 95% Confidence Intervals	0.012 ± 0.029
Sensitivity	0.005
Positive Predictive Value	0.200
Nr of predictions	8

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
3AMU_B	tRNA links to Rfam database...	0.00	0.00	0.00	0	1157	0	0	0	0	19
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.