CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	ContextFold		RNASampler(seed)
MCC	0.477	>	0.390
Average MCC ± 95% Confidence Intervals	0.439 ± 0.256	>	0.380 ± 0.216
Sensitivity	0.475	>	0.323
Positive Predictive Value	0.487	>	0.481
Total TP	75	>	51
Total TN	20838	<	20886
Total FP	126	>	85
Total FP CONTRA	30	>	16
Total FP INCONS	49	>	39
Total FP COMP	47	>	30
Total FN	83	<	107
P-value	0.0

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

Total Scores
MCC	0.477
Average MCC ± 95% Confidence Intervals	0.439 ± 0.256
Sensitivity	0.475
Positive Predictive Value	0.487
Nr of predictions	7

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...	0.58	0.56	0.63	10	512	6	0	6	0	8
3J3E_8	5_8S_rRNA links to Rfam database...	-0.01	0.00	0.00	0	2722	29	12	8	9	15
3J3F_8	5_8S_rRNA links to Rfam database...	0.36	0.42	0.31	8	4735	32	9	9	14	11
3W3S_B	tRNA-Sec links to Rfam database...	0.87	0.85	0.90	28	1958	4	0	3	1	5
3ZEX_C	5_8S_rRNA links to Rfam database...	0.44	0.41	0.48	12	5349	23	4	9	10	17
4A1C_2	5_8S_rRNA links to Rfam database...	0.26	0.25	0.28	5	4498	26	3	10	13	15
4JF2_A	preQ1-II links to Rfam database...	0.57	0.50	0.67	12	1064	6	2	4	0	12

Total Scores
MCC	0.390
Average MCC ± 95% Confidence Intervals	0.380 ± 0.216
Sensitivity	0.323
Positive Predictive Value	0.481
Nr of predictions	7

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
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
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.