CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	Contrafold		Afold
MCC	0.630	>	0.493
Average MCC ± 95% Confidence Intervals	0.668 ± 0.114	>	0.559 ± 0.134
Sensitivity	0.658	>	0.537
Positive Predictive Value	0.602	>	0.453
Total TP	1714	>	1397
Total TN	4971131	>	4970891
Total FP	1615	<	2083
Total FP CONTRA	415	<	525
Total FP INCONS	716	<	1163
Total FP COMP	484	>	395
Total FN	889	<	1206
P-value	5.1503931209e-08

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

Total Scores
MCC	0.630
Average MCC ± 95% Confidence Intervals	0.668 ± 0.114
Sensitivity	0.658
Positive Predictive Value	0.602
Nr of predictions	24

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2KFC_A	-	0.71	0.63	0.83	5	230	1	1	0	0	3
2LC8_A	GP_knot1 links to Rfam database...	0.46	0.39	0.58	7	516	5	3	2	0	11
2RP0_A	-	0.84	0.71	1.00	5	111	0	0	0	0	2
2WDL_A	-	0.69	0.71	0.68	556	1444510	320	75	181	64	232
2ZZN_D	tRNA links to Rfam database...	0.93	0.95	0.91	21	961	3	2	0	1	1
3A2K_C	tRNA links to Rfam database...	0.49	0.55	0.46	12	1082	14	3	11	0	10
3A3A_A	tRNA-Sec links to Rfam database...	0.97	0.93	1.00	28	1472	0	0	0	0	2
3ADB_C	-	0.98	0.97	1.00	32	1787	0	0	0	0	1
3GCA_A	-	0.76	0.71	0.83	5	152	1	1	0	0	2
3IVN_B	Purine links to Rfam database...	0.91	0.83	1.00	19	884	0	0	0	0	4
3IWN_A	c-di-GMP-I links to Rfam database...	0.86	0.79	0.96	22	1449	1	0	1	0	6
3IYQ_A	tmRNA links to Rfam database...	0.28	0.39	0.20	20	22341	95	44	35	16	31
3IZ4_A	tmRNA links to Rfam database...	0.57	0.58	0.57	55	25440	49	18	23	8	40
3JYV_7	tRNA links to Rfam database...	-0.02	0.00	0.00	0	1091	20	4	16	0	20
3JYX_5	-	0.43	0.50	0.37	240	1968358	697	172	232	293	241
3KIY_A	-	0.70	0.71	0.69	561	1485072	329	73	174	82	225
3LA5_A	Purine links to Rfam database...	0.91	0.84	1.00	21	933	0	0	0	0	4
3NKB_B	-	0.63	0.68	0.59	13	713	9	0	9	0	6
3NPB_A	SAM links to Rfam database...	0.86	0.84	0.89	31	2243	9	1	3	5	6
3O58_3	5_8S_rRNA links to Rfam database...	0.32	0.36	0.29	8	4736	21	7	13	1	14
3RKF_A	Purine links to Rfam database...	0.87	0.83	0.91	20	844	2	2	0	0	4
3U4M_B	-	0.81	0.77	0.85	17	1256	5	0	3	2	5
4A1C_2	5_8S_rRNA links to Rfam database...	0.21	0.25	0.19	5	4489	33	9	13	11	15
4ENB_A	crcB links to Rfam database...	0.85	0.73	1.00	11	461	1	0	0	1	4

Total Scores
MCC	0.493
Average MCC ± 95% Confidence Intervals	0.559 ± 0.134
Sensitivity	0.537
Positive Predictive Value	0.453
Nr of predictions	24

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2KFC_A	-	-0.03	0.00	0.00	0	228	8	1	7	0	8
2LC8_A	GP_knot1 links to Rfam database...	0.64	0.61	0.69	11	512	6	0	5	1	7
2RP0_A	-	0.76	0.71	0.83	5	110	1	0	1	0	2
2WDL_A	-	0.52	0.54	0.50	426	1444477	465	78	341	46	362
2ZZN_D	tRNA links to Rfam database...	0.91	0.91	0.91	20	962	3	2	0	1	2
3A2K_C	tRNA links to Rfam database...	0.46	0.50	0.44	11	1083	14	3	11	0	11
3A3A_A	tRNA-Sec links to Rfam database...	0.93	0.87	1.00	26	1474	0	0	0	0	4
3ADB_C	-	0.85	0.85	0.85	28	1786	6	0	5	1	5
3GCA_A	-	-0.04	0.00	0.00	0	151	9	1	6	2	7
3IVN_B	Purine links to Rfam database...	0.91	0.83	1.00	19	884	0	0	0	0	4
3IWN_A	c-di-GMP-I links to Rfam database...	0.67	0.68	0.68	19	1444	9	1	8	0	9
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
3JYV_7	tRNA links to Rfam database...	-0.02	0.00	0.00	0	1088	23	4	19	0	20
3JYX_5	-	0.34	0.44	0.27	210	1968232	793	260	300	233	271
3KIY_A	-	0.53	0.55	0.51	430	1485031	475	81	338	56	356
3LA5_A	Purine links to Rfam database...	0.91	0.84	1.00	21	933	0	0	0	0	4
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
4A1C_2	5_8S_rRNA links to Rfam database...	0.19	0.25	0.15	5	4483	43	11	17	15	15
4ENB_A	crcB links to Rfam database...	0.81	0.73	0.92	11	460	3	0	1	2	4

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