CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	TurboFold(seed)		NanoFolder
MCC	0.448	>	0.318
Average MCC ± 95% Confidence Intervals	0.449 ± 0.303	>	0.345 ± 0.247
Sensitivity	0.464	>	0.421
Positive Predictive Value	0.442	>	0.252
Total TP	65	>	59
Total TN	15415	>	15328
Total FP	122	<	224
Total FP CONTRA	30	<	66
Total FP INCONS	52	<	109
Total FP COMP	40	<	49
Total FN	75	<	81
P-value	0.0

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

Total Scores
MCC	0.448
Average MCC ± 95% Confidence Intervals	0.449 ± 0.303
Sensitivity	0.464
Positive Predictive Value	0.442
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	513	15	3	12	0	18
3J3E_8	5_8S_rRNA links to Rfam database...	0.27	0.33	0.23	5	2720	28	6	11	11	10
3J3F_8	5_8S_rRNA links to Rfam database...	0.42	0.53	0.34	10	4732	35	9	10	16	9
4A1C_2	5_8S_rRNA links to Rfam database...	0.20	0.25	0.17	5	4486	37	9	16	12	15
4AOB_A	SAM links to Rfam database...	0.67	0.59	0.77	17	1415	6	2	3	1	12
4ENC_A	crcB links to Rfam database...	0.73	0.60	0.90	9	486	1	1	0	0	6
4JF2_A	preQ1-II links to Rfam database...	0.89	0.79	1.00	19	1063	0	0	0	0	5

Total Scores
MCC	0.318
Average MCC ± 95% Confidence Intervals	0.345 ± 0.247
Sensitivity	0.421
Positive Predictive Value	0.252
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...	0.54	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
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

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