CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	MXScarna(seed)		NanoFolder
MCC	0.498	>	0.295
Average MCC ± 95% Confidence Intervals	0.434 ± 0.206	>	0.324 ± 0.213
Sensitivity	0.445	>	0.382
Positive Predictive Value	0.566	>	0.241
Total TP	77	>	66
Total TN	17415	>	17277
Total FP	96	<	258
Total FP CONTRA	16	<	68
Total FP INCONS	43	<	140
Total FP COMP	37	<	50
Total FN	96	<	107
P-value	0.0

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

Total Scores
MCC	0.498
Average MCC ± 95% Confidence Intervals	0.434 ± 0.206
Sensitivity	0.445
Positive Predictive Value	0.566
Nr of predictions	8

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	12	0	10	2	18
3J3E_8	5_8S_rRNA links to Rfam database...	0.23	0.20	0.27	3	2731	14	3	5	6	12
3J3F_8	5_8S_rRNA links to Rfam database...	0.48	0.47	0.50	9	4743	21	5	4	12	10
3W3S_B	tRNA-Sec links to Rfam database...	0.74	0.70	0.79	23	1960	7	0	6	1	10
4A1C_2	5_8S_rRNA links to Rfam database...	0.45	0.40	0.50	8	4500	20	4	4	12	12
4AOB_A	SAM links to Rfam database...	0.71	0.69	0.74	20	1410	10	2	5	3	9
4ENC_A	crcB links to Rfam database...	0.48	0.40	0.60	6	486	4	1	3	0	9
4JF2_A	preQ1-II links to Rfam database...	0.41	0.33	0.53	8	1067	8	1	6	1	16

Total Scores
MCC	0.295
Average MCC ± 95% Confidence Intervals	0.324 ± 0.213
Sensitivity	0.382
Positive Predictive Value	0.241
Nr of predictions	8

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
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.