CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	RNASampler(seed)		PPfold(seed)
MCC	0.447	>	0.160
Average MCC ± 95% Confidence Intervals	0.421 ± 0.287	>	0.124 ± 0.195
Sensitivity	0.299	>	0.050
Positive Predictive Value	0.673	>	0.524
Total TP	66	>	11
Total TN	38299	<	38376
Total FP	45	<	47
Total FP CONTRA	1	>	0
Total FP INCONS	31	>	10
Total FP COMP	13	<	37
Total FN	155	<	210
P-value	0.0

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

Total Scores
MCC	0.447
Average MCC ± 95% Confidence Intervals	0.421 ± 0.287
Sensitivity	0.299
Positive Predictive Value	0.673
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...	-0.01	0.00	0.00	0	1530	10	0	10	0	20
3RKF_A	Purine links to Rfam database...	0.76	0.59	1.00	20	2191	0	0	0	0	14
3SD1_A	THF links to Rfam database...	0.60	0.38	0.94	16	3899	1	0	1	0	26
3W3S_B	tRNA-Sec links to Rfam database...	0.55	0.30	1.00	12	4741	1	0	0	1	28
3ZEX_C	5_8S_rRNA links to Rfam database...	0.32	0.19	0.53	10	14177	13	1	8	4	42
4A1C_2	5_8S_rRNA links to Rfam database...	0.31	0.24	0.40	8	11761	20	0	12	8	25

Total Scores
MCC	0.160
Average MCC ± 95% Confidence Intervals	0.124 ± 0.195
Sensitivity	0.050
Positive Predictive Value	0.524
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...	0.47	0.30	0.75	6	1532	2	0	2	0	14
3RKF_A	Purine links to Rfam database...	0.00	0.00	0.00	0	2211	0	0	0	0	34
3SD1_A	THF links to Rfam database...	0.00	0.00	0.00	0	3916	0	0	0	0	42
3W3S_B	tRNA-Sec links to Rfam database...	0.00	0.00	0.00	0	4753	0	0	0	0	40
3ZEX_C	5_8S_rRNA links to Rfam database...	0.20	0.08	0.50	4	14188	22	0	4	18	48
4A1C_2	5_8S_rRNA links to Rfam database...	0.08	0.03	0.20	1	11776	23	0	4	19	32

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