CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	NanoFolder		Mastr(seed)
MCC	0.340	>	0.075
Average MCC ± 95% Confidence Intervals	0.372 ± 0.215	>	0.023 ± 0.053
Sensitivity	0.438	>	0.016
Positive Predictive Value	0.277	<	0.375
Total TP	84	>	3
Total TN	18216	<	18511
Total FP	269	>	5
Total FP CONTRA	77	>	0
Total FP INCONS	142	>	5
Total FP COMP	50	>	0
Total FN	108	<	189
P-value	0.0

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

Total Scores
MCC	0.340
Average MCC ± 95% Confidence Intervals	0.372 ± 0.215
Sensitivity	0.438
Positive Predictive Value	0.277
Nr of predictions	9

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
3J3D_C	tRNA links to Rfam database...	0.76	0.95	0.62	18	939	11	9	2	0	1
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
4AOB_A	SAM links to Rfam database...	0.39	0.41	0.39	12	1406	20	4	15	1	17
4ENC_A	crcB links to Rfam database...	0.66	0.73	0.61	11	478	9	2	5	2	4
4JF2_A	preQ1-II links to Rfam database...	0.55	0.67	0.47	16	1048	19	9	9	1	8

Total Scores
MCC	0.075
Average MCC ± 95% Confidence Intervals	0.023 ± 0.053
Sensitivity	0.016
Positive Predictive Value	0.375
Nr of predictions	9

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
3J3D_C	tRNA links to Rfam database...	0.00	0.00	0.00	0	968	0	0	0	0	19
3J3E_8	5_8S_rRNA links to Rfam database...	0.00	0.00	0.00	0	2742	0	0	0	0	15
3J3F_8	5_8S_rRNA links to Rfam database...	0.00	0.00	0.00	0	4761	0	0	0	0	19
3W3S_B	tRNA-Sec links to Rfam database...	0.00	0.00	0.00	0	1989	0	0	0	0	33
4A1C_2	5_8S_rRNA links to Rfam database...	0.00	0.00	0.00	0	4516	0	0	0	0	20
4AOB_A	SAM links to Rfam database...	0.00	0.00	0.00	0	1437	0	0	0	0	29
4ENC_A	crcB links to Rfam database...	0.00	0.00	0.00	0	496	0	0	0	0	15
4JF2_A	preQ1-II links to Rfam database...	0.21	0.13	0.38	3	1074	5	0	5	0	21

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