CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	IPknot		NanoFolder
MCC	0.567	>	0.406
Average MCC ± 95% Confidence Intervals	0.542 ± 0.170	>	0.450 ± 0.163
Sensitivity	0.564	>	0.516
Positive Predictive Value	0.580	>	0.333
Total TP	141	>	129
Total TN	20938	>	20794
Total FP	137	<	311
Total FP CONTRA	35	<	98
Total FP INCONS	67	<	160
Total FP COMP	35	<	53
Total FN	109	<	121
P-value	1.74172190343e-08

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

Total Scores
MCC	0.567
Average MCC ± 95% Confidence Intervals	0.542 ± 0.170
Sensitivity	0.564
Positive Predictive Value	0.580
Nr of predictions	13

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	0.33	0.55	6	517	5	1	4	0	12
2M58_A	-	0.71	0.58	0.88	7	536	1	1	0	0	5
3J3D_C	tRNA links to Rfam database...	0.52	0.53	0.53	10	949	9	3	6	0	9
3J3E_8	5_8S_rRNA links to Rfam database...	-0.01	0.00	0.00	0	2723	25	5	14	6	15
3J3F_8	5_8S_rRNA links to Rfam database...	0.36	0.47	0.28	9	4729	40	11	12	17	10
3U4M_B	-	0.91	0.91	0.91	20	1254	3	2	0	1	2
3W3S_B	tRNA-Sec links to Rfam database...	0.94	0.91	0.97	30	1958	2	0	1	1	3
4A1C_2	5_8S_rRNA links to Rfam database...	0.23	0.25	0.22	5	4493	26	8	10	8	15
4AOB_A	SAM links to Rfam database...	0.50	0.48	0.54	14	1411	13	3	9	1	15
4ATO_G	-	0.49	0.57	0.44	4	211	6	0	5	1	3
4ENC_A	crcB links to Rfam database...	0.59	0.53	0.67	8	484	4	0	4	0	7
4JF2_A	preQ1-II links to Rfam database...	0.96	0.96	0.96	23	1058	1	1	0	0	1
4JRC_A	-	0.45	0.29	0.71	5	615	2	0	2	0	12

Total Scores
MCC	0.406
Average MCC ± 95% Confidence Intervals	0.450 ± 0.163
Sensitivity	0.516
Positive Predictive Value	0.333
Nr of predictions	13

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
2M58_A	-	0.45	0.58	0.37	7	525	13	6	6	1	5
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
3U4M_B	-	0.77	0.91	0.67	20	1246	12	6	4	2	2
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
4ATO_G	-	0.72	1.00	0.54	7	207	6	6	0	0	0
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
4JRC_A	-	0.56	0.65	0.50	11	600	11	3	8	0	6

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