CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	Afold		Fold
MCC	0.435	>	0.412
Average MCC ± 95% Confidence Intervals	0.516 ± 0.120	>	0.425 ± 0.161
Sensitivity	0.481	>	0.450
Positive Predictive Value	0.396	>	0.378
Total TP	378	>	354
Total TN	491744	<	491763
Total FP	692	<	696
Total FP CONTRA	187	>	182
Total FP INCONS	390	<	400
Total FP COMP	115	>	114
Total FN	408	<	432
P-value	2.39162260866e-08

Comparison of performance of Afold and Fold. 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 Afold and Fold).
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 Afold and Fold).
Comparison of average Matthews Correlation Coefficients (MCCs) for Afold and Fold. 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 Afold and Fold).

Total Scores
MCC	0.435
Average MCC ± 95% Confidence Intervals	0.516 ± 0.120
Sensitivity	0.481
Positive Predictive Value	0.396
Nr of predictions	17

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...	0.64	0.61	0.69	11	512	6	0	5	1	7
2M58_A	-	0.40	0.42	0.42	5	532	8	1	6	1	7
3ADB_C	-	0.85	0.85	0.85	28	1786	6	0	5	1	5
3IYQ_A	tmRNA links to Rfam database...	0.23	0.33	0.17	17	22339	97	47	37	13	34
3IZ4_A	tmRNA links to Rfam database...	0.52	0.57	0.48	54	25423	63	27	32	4	41
3J3E_8	5_8S_rRNA links to Rfam database...	0.26	0.33	0.21	5	2718	31	6	13	12	10
3NKB_B	-	0.69	0.74	0.67	14	714	7	0	7	0	5
3NPB_A	SAM links to Rfam database...	0.82	0.73	0.93	27	2249	6	0	2	4	10
3O58_3	5_8S_rRNA links to Rfam database...	0.41	0.50	0.34	11	4732	38	6	15	17	11
3RKF_A	Purine links to Rfam database...	0.91	0.83	1.00	20	846	0	0	0	0	4
3U4M_B	-	0.49	0.55	0.46	12	1250	14	3	11	0	10
3W3S_B	tRNA-Sec links to Rfam database...	0.55	0.55	0.56	18	1957	15	4	10	1	15
3ZEX_B	-	0.34	0.38	0.31	132	420926	337	77	217	43	214
4A1C_2	5_8S_rRNA links to Rfam database...	0.19	0.25	0.15	5	4483	43	11	17	15	15
4ATO_G	-	0.38	0.43	0.38	3	212	6	5	0	1	4
4ENB_A	crcB links to Rfam database...	0.81	0.73	0.92	11	460	3	0	1	2	4
4JRC_A	-	0.27	0.29	0.29	5	605	12	0	12	0	12

Total Scores
MCC	0.412
Average MCC ± 95% Confidence Intervals	0.425 ± 0.161
Sensitivity	0.450
Positive Predictive Value	0.378
Nr of predictions	17

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	513	15	3	12	0	18
2M58_A	-	-0.02	0.00	0.00	0	529	15	0	15	0	12
3ADB_C	-	0.86	0.85	0.88	28	1787	4	0	4	0	5
3IYQ_A	tmRNA links to Rfam database...	0.24	0.33	0.18	17	22345	95	40	38	17	34
3IZ4_A	tmRNA links to Rfam database...	0.60	0.61	0.59	58	25437	47	16	25	6	37
3J3E_8	5_8S_rRNA links to Rfam database...	-0.01	0.00	0.00	0	2719	34	5	18	11	15
3NKB_B	-	0.41	0.42	0.42	8	716	11	4	7	0	11
3NPB_A	SAM links to Rfam database...	0.77	0.73	0.82	27	2245	11	0	6	5	10
3O58_3	5_8S_rRNA links to Rfam database...	0.39	0.50	0.31	11	4728	41	9	16	16	11
3RKF_A	Purine links to Rfam database...	0.91	0.83	1.00	20	846	0	0	0	0	4
3U4M_B	-	0.58	0.59	0.59	13	1254	9	2	7	0	9
3W3S_B	tRNA-Sec links to Rfam database...	0.94	0.91	0.97	30	1958	2	0	1	1	3
3ZEX_B	-	0.32	0.36	0.29	123	420926	346	87	216	43	223
4A1C_2	5_8S_rRNA links to Rfam database...	0.19	0.25	0.15	5	4482	43	11	18	14	15
4ATO_G	-	0.38	0.43	0.38	3	212	5	5	0	0	4
4ENB_A	crcB links to Rfam database...	0.37	0.33	0.45	5	461	7	0	6	1	10
4JRC_A	-	0.34	0.35	0.35	6	605	11	0	11	0	11

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