CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	MaxExpect		Afold
MCC	0.632	>	0.534
Average MCC ± 95% Confidence Intervals	0.607 ± 0.145	>	0.590 ± 0.142
Sensitivity	0.648	>	0.563
Positive Predictive Value	0.616	>	0.507
Total TP	817	>	710
Total TN	1555332	>	1555257
Total FP	624	<	804
Total FP CONTRA	166	<	183
Total FP INCONS	343	<	508
Total FP COMP	115	>	113
Total FN	443	<	550
P-value	2.86595104665e-08

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

Total Scores
MCC	0.632
Average MCC ± 95% Confidence Intervals	0.607 ± 0.145
Sensitivity	0.648
Positive Predictive Value	0.616
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
3A2K_C	tRNA links to Rfam database...	0.47	0.50	0.46	11	1084	13	3	10	0	11
3ADB_C	-	0.86	0.85	0.88	28	1787	4	0	4	0	5
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...	0.80	0.79	0.81	22	1445	6	1	4	1	6
3IYQ_A	tmRNA links to Rfam database...	0.24	0.33	0.17	17	22342	96	41	40	15	34
3IZ4_A	tmRNA links to Rfam database...	0.61	0.61	0.62	58	25442	42	14	22	6	37
3JYV_7	tRNA links to Rfam database...	0.48	0.45	0.53	9	1094	9	3	5	1	11
3KIY_A	-	0.67	0.68	0.66	531	1485073	336	81	195	60	255
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...	0.77	0.73	0.82	27	2245	10	0	6	4	10
3O58_3	5_8S_rRNA links to Rfam database...	0.40	0.50	0.33	11	4731	36	8	14	14	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
4A1C_2	5_8S_rRNA links to Rfam database...	0.19	0.25	0.16	5	4484	41	10	17	14	15
4ENB_A	crcB links to Rfam database...	0.85	0.73	1.00	11	461	0	0	0	0	4

Total Scores
MCC	0.534
Average MCC ± 95% Confidence Intervals	0.590 ± 0.142
Sensitivity	0.563
Positive Predictive Value	0.507
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
3A2K_C	tRNA links to Rfam database...	0.46	0.50	0.44	11	1083	14	3	11	0	11
3ADB_C	-	0.85	0.85	0.85	28	1786	6	0	5	1	5
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
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.