CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	ProbKnot		Afold
MCC	0.424	>	0.419
Average MCC ± 95% Confidence Intervals	0.442 ± 0.176	<	0.496 ± 0.120
Sensitivity	0.463	<	0.465
Positive Predictive Value	0.390	>	0.380
Total TP	349	<	350
Total TN	489984	>	489958
Total FP	669	<	686
Total FP CONTRA	182	<	187
Total FP INCONS	365	<	385
Total FP COMP	122	>	114
Total FN	404	>	403
P-value	3.42322841337e-08

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

Total Scores
MCC	0.424
Average MCC ± 95% Confidence Intervals	0.442 ± 0.176
Sensitivity	0.463
Positive Predictive Value	0.390
Nr of predictions	16

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
3IYQ_A	tmRNA links to Rfam database...	0.24	0.33	0.18	17	22346	97	41	36	20	34
3IZ4_A	tmRNA links to Rfam database...	0.59	0.61	0.57	58	25435	49	17	26	6	37
3J3E_8	5_8S_rRNA links to Rfam database...	-0.01	0.00	0.00	0	2718	37	6	18	13	15
3NKB_B	-	0.69	0.74	0.67	14	714	7	0	7	0	5
3NPB_A	SAM links to Rfam database...	0.79	0.73	0.87	27	2247	9	0	4	5	10
3O58_3	5_8S_rRNA links to Rfam database...	0.38	0.50	0.29	11	4726	42	10	17	15	11
3RKF_A	Purine links to Rfam database...	0.87	0.83	0.91	20	844	2	2	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...	0.98	0.97	1.00	32	1957	1	0	0	1	1
3ZEX_B	-	0.35	0.38	0.33	133	420946	320	82	191	47	213
4A1C_2	5_8S_rRNA links to Rfam database...	0.17	0.25	0.13	5	4477	49	13	21	15	15
4ATO_G	-	0.38	0.43	0.38	3	212	5	5	0	0	4
4ENB_A	crcB links to Rfam database...	0.81	0.73	0.92	11	460	1	1	0	0	4
4JRC_A	-	0.28	0.29	0.31	5	606	11	0	11	0	12

Total Scores
MCC	0.419
Average MCC ± 95% Confidence Intervals	0.496 ± 0.120
Sensitivity	0.465
Positive Predictive Value	0.380
Nr of predictions	16

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
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

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