CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	ProbKnot		Vsfold5
MCC	0.564	>	0.469
Average MCC ± 95% Confidence Intervals	0.574 ± 0.141	>	0.513 ± 0.161
Sensitivity	0.613	>	0.481
Positive Predictive Value	0.525	>	0.463
Total TP	294	>	231
Total TN	73592	<	73653
Total FP	341	>	322
Total FP CONTRA	114	>	99
Total FP INCONS	152	<	169
Total FP COMP	75	>	54
Total FN	186	<	249
P-value	2.36983135185e-08

Comparison of performance of ProbKnot and Vsfold5. 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 Vsfold5).
Comparison of average Matthews Correlation Coefficients (MCCs) for ProbKnot and Vsfold5. 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 Vsfold5).

Total Scores
MCC	0.564
Average MCC ± 95% Confidence Intervals	0.574 ± 0.141
Sensitivity	0.613
Positive Predictive Value	0.525
Nr of predictions	16

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2KRL_A	-	0.82	0.87	0.77	20	1998	15	6	0	9	3
2LC8_A	GP_knot1 links to Rfam database...	-0.03	0.00	0.00	0	513	15	3	12	0	18
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
3J0L_a	-	0.60	0.64	0.58	7	399	6	4	1	1	4
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
3PDR_A	ykoK links to Rfam database...	0.88	0.92	0.85	46	4786	10	5	3	2	4
3RKF_A	Purine links to Rfam database...	0.87	0.83	0.91	20	844	2	2	0	0	4
3SD1_A	THF links to Rfam database...	0.66	0.69	0.65	20	1502	11	6	5	0	9
3U4M_B	-	0.58	0.59	0.59	13	1254	9	2	7	0	9
4A1C_2	5_8S_rRNA links to Rfam database...	0.17	0.25	0.13	5	4477	49	13	21	15	15
4AOB_A	SAM links to Rfam database...	0.60	0.59	0.63	17	1410	11	4	6	1	12
4ENB_A	crcB links to Rfam database...	0.81	0.73	0.92	11	460	1	1	0	0	4
4ENC_A	crcB links to Rfam database...	0.52	0.53	0.53	8	481	8	0	7	1	7

Total Scores
MCC	0.469
Average MCC ± 95% Confidence Intervals	0.513 ± 0.161
Sensitivity	0.481
Positive Predictive Value	0.463
Nr of predictions	16

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2KRL_A	-	0.71	0.78	0.64	18	1996	13	8	2	3	5
2LC8_A	GP_knot1 links to Rfam database...	-0.03	0.00	0.00	0	515	13	0	13	0	18
3IYQ_A	tmRNA links to Rfam database...	0.30	0.37	0.24	19	22361	71	36	24	11	32
3IZ4_A	tmRNA links to Rfam database...	0.31	0.31	0.33	29	25448	65	14	45	6	66
3J0L_a	-	0.39	0.36	0.44	4	402	6	4	1	1	7
3NKB_B	-	0.69	0.74	0.67	14	714	7	0	7	0	5
3NPB_A	SAM links to Rfam database...	0.62	0.54	0.71	20	2250	10	1	7	2	17
3O58_3	5_8S_rRNA links to Rfam database...	0.51	0.59	0.45	13	4735	28	11	5	12	9
3PDR_A	ykoK links to Rfam database...	0.69	0.64	0.74	32	4797	13	3	8	2	18
3RKF_A	Purine links to Rfam database...	0.90	0.92	0.88	22	841	3	3	0	0	2
3SD1_A	THF links to Rfam database...	0.13	0.14	0.15	4	1507	22	5	17	0	25
3U4M_B	-	0.49	0.55	0.46	12	1250	14	3	11	0	10
4A1C_2	5_8S_rRNA links to Rfam database...	0.33	0.40	0.28	8	4487	37	8	13	16	12
4AOB_A	SAM links to Rfam database...	0.21	0.21	0.25	6	1413	19	2	16	1	23
4ENB_A	crcB links to Rfam database...	1.00	1.00	1.00	15	457	0	0	0	0	0
4ENC_A	crcB links to Rfam database...	0.97	1.00	0.94	15	480	1	1	0	0	0

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