CompaRNA - on-line benchmarks of RNA structure prediction methods

FAQ

Metric	CentroidAlifold(seed)		NanoFolder
MCC	0.677	>	0.340
Average MCC ± 95% Confidence Intervals	0.593 ± 0.206	>	0.372 ± 0.215
Sensitivity	0.495	>	0.438
Positive Predictive Value	0.931	>	0.277
Total TP	95	>	84
Total TN	18417	>	18216
Total FP	15	<	269
Total FP CONTRA	5	<	77
Total FP INCONS	2	<	142
Total FP COMP	8	<	50
Total FN	97	<	108
P-value	0.0

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

Total Scores
MCC	0.677
Average MCC ± 95% Confidence Intervals	0.593 ± 0.206
Sensitivity	0.495
Positive Predictive Value	0.931
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...	0.56	0.32	1.00	6	962	0	0	0	0	13
3J3E_8	5_8S_rRNA links to Rfam database...	0.39	0.20	0.75	3	2738	1	1	0	0	12
3J3F_8	5_8S_rRNA links to Rfam database...	0.62	0.47	0.82	9	4750	4	2	0	2	10
3W3S_B	tRNA-Sec links to Rfam database...	0.80	0.70	0.92	23	1964	4	0	2	2	10
4A1C_2	5_8S_rRNA links to Rfam database...	0.60	0.40	0.89	8	4507	3	1	0	2	12
4AOB_A	SAM links to Rfam database...	0.89	0.79	1.00	23	1414	2	0	0	2	6
4ENC_A	crcB links to Rfam database...	0.73	0.53	1.00	8	488	0	0	0	0	7
4JF2_A	preQ1-II links to Rfam database...	0.76	0.63	0.94	15	1066	1	1	0	0	9

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

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