CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	MCFold		NanoFolder
MCC	0.529	>	0.373
Average MCC ± 95% Confidence Intervals	0.496 ± 0.247	>	0.403 ± 0.196
Sensitivity	0.552	>	0.397
Positive Predictive Value	0.514	>	0.359
Total TP	128	>	92
Total TN	33578	>	33571
Total FP	154	<	173
Total FP CONTRA	14	<	26
Total FP INCONS	107	<	138
Total FP COMP	33	>	9
Total FN	104	<	140
P-value	0.0

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

Total Scores
MCC	0.529
Average MCC ± 95% Confidence Intervals	0.496 ± 0.247
Sensitivity	0.552
Positive Predictive Value	0.514
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...	0.41	0.45	0.39	9	1517	16	0	14	2	11
2LKR_A	-	0.93	0.92	0.95	36	6067	14	0	2	12	3
3J16_L	tRNA links to Rfam database...	0.45	0.47	0.44	14	2743	19	1	17	1	16
3U4M_B	-	0.59	0.59	0.59	22	3123	15	0	15	0	15
4A1C_3	5S_rRNA links to Rfam database...	0.68	0.67	0.71	36	7089	17	1	14	2	18
4A1C_2	5_8S_rRNA links to Rfam database...	0.13	0.15	0.11	5	11735	56	10	31	15	28
4ENC_A	crcB links to Rfam database...	0.28	0.32	0.27	6	1304	17	2	14	1	13

Total Scores
MCC	0.373
Average MCC ± 95% Confidence Intervals	0.403 ± 0.196
Sensitivity	0.397
Positive Predictive Value	0.359
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...	0.52	0.55	0.50	11	1518	11	0	11	0	9
2LKR_A	-	0.29	0.33	0.25	13	6054	38	8	30	0	26
3J16_L	tRNA links to Rfam database...	0.36	0.37	0.37	11	2745	19	3	16	0	19
3U4M_B	-	0.61	0.57	0.66	21	3128	11	1	10	0	16
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
4ENC_A	crcB links to Rfam database...	0.57	0.58	0.58	11	1307	9	0	8	1	8

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