CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	MCFold		NanoFolder
MCC	0.401	>	0.294
Average MCC ± 95% Confidence Intervals	0.380 ± 0.118	>	0.346 ± 0.100
Sensitivity	0.400	>	0.311
Positive Predictive Value	0.409	>	0.286
Total TP	285	>	222
Total TN	110996	>	110917
Total FP	488	<	591
Total FP CONTRA	43	<	73
Total FP INCONS	368	<	480
Total FP COMP	77	>	38
Total FN	428	<	491
P-value	4.98172311752e-08

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).
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 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	0.401
Average MCC ± 95% Confidence Intervals	0.380 ± 0.118
Sensitivity	0.400
Positive Predictive Value	0.409
Nr of predictions	20

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
2M58_A	-	0.20	0.24	0.18	4	1631	19	2	16	1	13
3J16_L	tRNA links to Rfam database...	0.45	0.47	0.44	14	2743	19	1	17	1	16
3J2L_3	5S_rRNA links to Rfam database...	0.58	0.57	0.60	30	7825	23	2	18	3	23
3J3D_C	tRNA links to Rfam database...	0.42	0.43	0.43	12	2747	18	2	14	2	16
3J3E_7	5S_rRNA links to Rfam database...	0.40	0.39	0.42	21	7090	29	3	26	0	33
3J3E_8	5_8S_rRNA links to Rfam database...	0.12	0.12	0.12	4	7470	46	3	26	17	29
3J3F_7	5S_rRNA links to Rfam database...	0.74	0.74	0.74	37	7210	17	2	11	4	13
3J3F_8	5_8S_rRNA links to Rfam database...	0.13	0.17	0.11	6	12191	61	9	40	12	30
3U4M_B	-	0.59	0.59	0.59	22	3123	15	0	15	0	15
3ZEX_D	5S_rRNA links to Rfam database...	0.17	0.18	0.18	9	6970	42	4	38	0	40
3ZEX_G	-	0.00	0.00	0.00	0	16456	15	1	14	0	74
3ZND_W	tRNA links to Rfam database...	0.19	0.22	0.18	5	2975	26	1	22	3	18
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
4ATO_G	-	0.30	0.30	0.33	3	519	8	0	6	2	7
4ENC_A	crcB links to Rfam database...	0.28	0.32	0.27	6	1304	17	2	14	1	13
4JF2_A	preQ1-II links to Rfam database...	0.66	0.68	0.66	21	2818	11	0	11	0	10
4JRC_A	-	0.20	0.22	0.21	5	1516	19	0	19	0	18

Total Scores
MCC	0.294
Average MCC ± 95% Confidence Intervals	0.346 ± 0.100
Sensitivity	0.311
Positive Predictive Value	0.286
Nr of predictions	20

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
2M58_A	-	0.43	0.47	0.40	8	1633	12	4	8	0	9
3J16_L	tRNA links to Rfam database...	0.36	0.37	0.37	11	2745	19	3	16	0	19
3J2L_3	5S_rRNA links to Rfam database...	0.11	0.11	0.12	6	7824	46	3	42	1	47
3J3D_C	tRNA links to Rfam database...	0.70	0.71	0.69	20	2746	9	2	7	0	8
3J3E_7	5S_rRNA links to Rfam database...	0.35	0.33	0.37	18	7091	31	1	30	0	36
3J3E_8	5_8S_rRNA links to Rfam database...	0.00	0.00	0.00	0	7466	47	6	31	10	33
3J3F_7	5S_rRNA links to Rfam database...	0.17	0.18	0.17	9	7208	43	3	40	0	41
3J3F_8	5_8S_rRNA links to Rfam database...	0.27	0.33	0.22	12	12192	54	9	33	12	24
3U4M_B	-	0.61	0.57	0.66	21	3128	11	1	10	0	16
3ZEX_D	5S_rRNA links to Rfam database...	0.26	0.27	0.27	13	6972	36	1	35	0	36
3ZEX_G	-	0.05	0.05	0.05	4	16393	76	5	69	2	70
3ZND_W	tRNA links to Rfam database...	0.18	0.22	0.17	5	2973	29	6	19	4	18
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
4ATO_G	-	0.61	0.70	0.54	7	515	6	2	4	0	3
4ENC_A	crcB links to Rfam database...	0.57	0.58	0.58	11	1307	9	0	8	1	8
4JF2_A	preQ1-II links to Rfam database...	0.51	0.55	0.49	17	2815	18	5	13	0	14
4JRC_A	-	0.48	0.48	0.50	11	1518	11	0	11	0	12

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