CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	NanoFolder		PPfold(seed)
MCC	0.292	>	0.096
Average MCC ± 95% Confidence Intervals	0.324 ± 0.120	>	0.050 ± 0.095
Sensitivity	0.300	>	0.018
Positive Predictive Value	0.294	<	0.538
Total TP	120	>	7
Total TN	54670	<	55065
Total FP	300	>	25
Total FP CONTRA	31	>	0
Total FP INCONS	257	>	6
Total FP COMP	12	<	19
Total FN	280	<	393
P-value	1.95070920198e-08

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

Total Scores
MCC	0.292
Average MCC ± 95% Confidence Intervals	0.324 ± 0.120
Sensitivity	0.300
Positive Predictive Value	0.294
Nr of predictions	11

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...	0.52	0.55	0.50	11	1518	11	0	11	0	9
3J16_L	tRNA links to Rfam database...	0.36	0.37	0.37	11	2745	19	3	16	0	19
3J20_1	tRNA links to Rfam database...	0.41	0.48	0.37	11	2896	19	5	14	0	12
3J2L_3	5S_rRNA links to Rfam database...	0.11	0.11	0.12	6	7824	46	3	42	1	47
3UZL_B	tRNA links to Rfam database...	0.36	0.35	0.38	13	3536	21	3	18	0	24
3W3S_B	tRNA-Sec links to Rfam database...	0.17	0.18	0.18	7	4713	34	1	32	1	33
3ZEX_D	5S_rRNA links to Rfam database...	0.26	0.27	0.27	13	6972	36	1	35	0	36
4A1C_3	5S_rRNA links to Rfam database...	0.48	0.46	0.51	25	7091	24	2	22	0	29
4A1C_2	5_8S_rRNA links to Rfam database...	0.00	0.00	0.00	0	11728	61	12	41	8	33
4AOB_A	SAM links to Rfam database...	0.33	0.29	0.39	12	4340	20	1	18	1	30
4ENC_A	crcB links to Rfam database...	0.57	0.58	0.58	11	1307	9	0	8	1	8

Total Scores
MCC	0.096
Average MCC ± 95% Confidence Intervals	0.050 ± 0.095
Sensitivity	0.018
Positive Predictive Value	0.538
Nr of predictions	11

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...	0.47	0.30	0.75	6	1532	2	0	2	0	14
3J16_L	tRNA links to Rfam database...	0.00	0.00	0.00	0	2775	0	0	0	0	30
3J20_1	tRNA links to Rfam database...	0.00	0.00	0.00	0	2926	0	0	0	0	23
3J2L_3	5S_rRNA links to Rfam database...	0.00	0.00	0.00	0	7875	0	0	0	0	53
3UZL_B	tRNA links to Rfam database...	0.00	0.00	0.00	0	3570	0	0	0	0	37
3W3S_B	tRNA-Sec links to Rfam database...	0.00	0.00	0.00	0	4753	0	0	0	0	40
3ZEX_D	5S_rRNA links to Rfam database...	0.00	0.00	0.00	0	7021	0	0	0	0	49
4A1C_3	5S_rRNA links to Rfam database...	0.00	0.00	0.00	0	7140	0	0	0	0	54
4A1C_2	5_8S_rRNA links to Rfam database...	0.08	0.03	0.20	1	11776	23	0	4	19	32
4AOB_A	SAM links to Rfam database...	0.00	0.00	0.00	0	4371	0	0	0	0	42
4ENC_A	crcB links to Rfam database...	0.00	0.00	0.00	0	1326	0	0	0	0	19

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