CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	RNASampler(seed)		NanoFolder
MCC	0.390	>	0.244
Average MCC ± 95% Confidence Intervals	0.378 ± 0.269	>	0.257 ± 0.262
Sensitivity	0.326	<	0.333
Positive Predictive Value	0.477	>	0.191
Total TP	42	<	43
Total TN	15530	>	15393
Total FP	71	<	229
Total FP CONTRA	14	<	62
Total FP INCONS	32	<	120
Total FP COMP	25	<	47
Total FN	87	>	86
P-value	0.0

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

Total Scores
MCC	0.390
Average MCC ± 95% Confidence Intervals	0.378 ± 0.269
Sensitivity	0.326
Positive Predictive Value	0.477
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...	-0.03	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
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

Total Scores
MCC	0.244
Average MCC ± 95% Confidence Intervals	0.257 ± 0.262
Sensitivity	0.333
Positive Predictive Value	0.191
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...	0.54	0.61	0.50	11	506	11	1	10	0	7
3J3E_8	5_8S_rRNA links to Rfam database...	-0.01	0.00	0.00	0	2707	47	11	24	12	15
3J3F_8	5_8S_rRNA links to Rfam database...	0.30	0.47	0.19	9	4714	57	21	17	19	10
3W3S_B	tRNA-Sec links to Rfam database...	0.18	0.21	0.18	7	1949	34	2	31	1	26
4A1C_2	5_8S_rRNA links to Rfam database...	-0.01	0.00	0.00	0	4469	61	18	29	14	20
4JF2_A	preQ1-II links to Rfam database...	0.55	0.67	0.47	16	1048	19	9	9	1	8

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