CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	RNASampler(seed)		ProbKnot
MCC	0.640	>	0.621
Average MCC ± 95% Confidence Intervals	0.613 ± 0.258	<	0.631 ± 0.343
Sensitivity	0.551	<	0.680
Positive Predictive Value	0.754	>	0.576
Total TP	98	<	121
Total TN	13988	>	13908
Total FP	46	<	120
Total FP CONTRA	9	<	34
Total FP INCONS	23	<	55
Total FP COMP	14	<	31
Total FN	80	>	57
P-value	0.0

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

Total Scores
MCC	0.640
Average MCC ± 95% Confidence Intervals	0.613 ± 0.258
Sensitivity	0.551
Positive Predictive Value	0.754
Nr of predictions	8

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2L1F_B	Gammaretro_CES links to Rfam database...	0.84	0.71	1.00	17	774	0	0	0	0	7
2L1F_A	Gammaretro_CES links to Rfam database...	0.83	0.70	1.00	16	747	0	0	0	0	7
2L94_A	HIV_FE links to Rfam database...	0.70	0.56	0.91	10	346	2	0	1	1	8
2LC8_A	GP_knot1 links to Rfam database...	-0.03	0.00	0.00	0	518	10	0	10	0	18
3O58_3	5_8S_rRNA links to Rfam database...	0.54	0.50	0.58	11	4745	13	5	3	5	11
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...	0.72	0.55	0.94	16	1516	1	0	1	0	13
4A1C_2	5_8S_rRNA links to Rfam database...	0.40	0.40	0.40	8	4496	20	4	8	8	12

Total Scores
MCC	0.621
Average MCC ± 95% Confidence Intervals	0.631 ± 0.343
Sensitivity	0.680
Positive Predictive Value	0.576
Nr of predictions	8

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2L1F_B	Gammaretro_CES links to Rfam database...	1.00	1.00	1.00	24	767	0	0	0	0	0
2L1F_A	Gammaretro_CES links to Rfam database...	1.00	1.00	1.00	23	740	0	0	0	0	0
2L94_A	HIV_FE links to Rfam database...	1.00	1.00	1.00	18	339	1	0	0	1	0
2LC8_A	GP_knot1 links to Rfam database...	-0.03	0.00	0.00	0	513	15	3	12	0	18
3O58_3	5_8S_rRNA links to Rfam database...	0.38	0.50	0.29	11	4726	42	10	17	15	11
3RKF_A	Purine links to Rfam database...	0.87	0.83	0.91	20	844	2	2	0	0	4
3SD1_A	THF links to Rfam database...	0.66	0.69	0.65	20	1502	11	6	5	0	9
4A1C_2	5_8S_rRNA links to Rfam database...	0.17	0.25	0.13	5	4477	49	13	21	15	15

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