CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	CentroidAlifold(seed)		RNASampler(seed)
MCC	0.736	>	0.563
Average MCC ± 95% Confidence Intervals	0.664 ± 0.169	>	0.542 ± 0.178
Sensitivity	0.584	>	0.472
Positive Predictive Value	0.933	>	0.678
Total TP	167	>	135
Total TN	30379	>	30359
Total FP	21	<	99
Total FP CONTRA	9	<	21
Total FP INCONS	3	<	43
Total FP COMP	9	<	35
Total FN	119	<	151
P-value	2.10198558684e-08

Comparison of performance of CentroidAlifold(seed) and RNASampler(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(seed) and RNASampler(seed)).
Average Matthews Correlation Coefficients (MCC) with 95% confidence intervals (CIs) were plotted for different RNA families, for which at least 3 members were present in the benchmarking dataset. 'n' denotes the number of MCCs used to calculate the average and CI. See tables below for raw data (individual counts for CentroidAlifold(seed) and RNASampler(seed)).
Comparison of average Matthews Correlation Coefficients (MCCs) for CentroidAlifold(seed) and RNASampler(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(seed) and RNASampler(seed)).

Total Scores
MCC	0.736
Average MCC ± 95% Confidence Intervals	0.664 ± 0.169
Sensitivity	0.584
Positive Predictive Value	0.933
Nr of predictions	12

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...	0.00	0.00	0.00	0	528	0	0	0	0	18
3A3A_A	tRNA-Sec links to Rfam database...	0.95	0.90	1.00	27	1473	0	0	0	0	3
3IVN_B	Purine links to Rfam database...	0.86	0.83	0.90	19	882	2	2	0	0	4
3J3E_8	5_8S_rRNA links to Rfam database...	0.39	0.20	0.75	3	2738	1	1	0	0	12
3J3F_8	5_8S_rRNA links to Rfam database...	0.62	0.47	0.82	9	4750	4	2	0	2	10
3O58_3	5_8S_rRNA links to Rfam database...	0.68	0.50	0.92	11	4752	2	1	0	1	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...	0.85	0.76	0.96	22	1510	1	0	1	0	7
3W3S_B	tRNA-Sec links to Rfam database...	0.80	0.70	0.92	23	1964	4	0	2	2	10
3ZEX_C	5_8S_rRNA links to Rfam database...	0.56	0.34	0.91	10	5363	3	1	0	2	19
4A1C_2	5_8S_rRNA links to Rfam database...	0.60	0.40	0.89	8	4507	3	1	0	2	12
4JF2_A	preQ1-II links to Rfam database...	0.76	0.63	0.94	15	1066	1	1	0	0	9

Total Scores
MCC	0.563
Average MCC ± 95% Confidence Intervals	0.542 ± 0.178
Sensitivity	0.472
Positive Predictive Value	0.678
Nr of predictions	12

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	518	10	0	10	0	18
3A3A_A	tRNA-Sec links to Rfam database...	0.77	0.60	1.00	18	1482	0	0	0	0	12
3IVN_B	Purine links to Rfam database...	0.91	0.83	1.00	19	884	0	0	0	0	4
3J3E_8	5_8S_rRNA links to Rfam database...	0.18	0.20	0.18	3	2725	22	5	9	8	12
3J3F_8	5_8S_rRNA links to Rfam database...	0.47	0.47	0.47	9	4742	18	5	5	8	10
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
3W3S_B	tRNA-Sec links to Rfam database...	0.60	0.36	1.00	12	1977	1	0	0	1	21
3ZEX_C	5_8S_rRNA links to Rfam database...	0.39	0.31	0.50	9	5356	14	2	7	5	20
4A1C_2	5_8S_rRNA links to Rfam database...	0.40	0.40	0.40	8	4496	20	4	8	8	12
4JF2_A	preQ1-II links to Rfam database...	0.64	0.42	1.00	10	1072	0	0	0	0	14

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