CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	RNAfold		ProbKnot
MCC	0.583	>	0.564
Average MCC ± 95% Confidence Intervals	0.601 ± 0.142	>	0.574 ± 0.141
Sensitivity	0.627	>	0.613
Positive Predictive Value	0.548	>	0.525
Total TP	301	>	294
Total TN	73603	>	73592
Total FP	311	<	341
Total FP CONTRA	106	<	114
Total FP INCONS	142	<	152
Total FP COMP	63	<	75
Total FN	179	<	186
P-value	6.84390417318e-09

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

Total Scores
MCC	0.583
Average MCC ± 95% Confidence Intervals	0.601 ± 0.142
Sensitivity	0.627
Positive Predictive Value	0.548
Nr of predictions	16

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2KRL_A	-	0.91	0.87	0.95	20	2003	9	1	0	8	3
2LC8_A	GP_knot1 links to Rfam database...	0.64	0.61	0.69	11	512	5	0	5	0	7
3IYQ_A	tmRNA links to Rfam database...	0.24	0.33	0.17	17	22340	95	45	38	12	34
3IZ4_A	tmRNA links to Rfam database...	0.56	0.60	0.52	57	25426	57	26	27	4	38
3J0L_a	-	0.18	0.18	0.22	2	402	8	3	4	1	9
3NKB_B	-	0.69	0.74	0.67	14	714	7	0	7	0	5
3NPB_A	SAM links to Rfam database...	0.91	0.86	0.97	32	2245	5	1	0	4	5
3O58_3	5_8S_rRNA links to Rfam database...	0.41	0.50	0.34	11	4732	35	6	15	14	11
3PDR_A	ykoK links to Rfam database...	0.90	0.90	0.90	45	4790	7	2	3	2	5
3RKF_A	Purine links to Rfam database...	0.91	0.83	1.00	20	846	0	0	0	0	4
3SD1_A	THF links to Rfam database...	0.77	0.76	0.79	22	1505	6	4	2	0	7
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	4482	43	11	18	14	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...	0.85	0.73	1.00	11	461	2	0	0	2	4
4ENC_A	crcB links to Rfam database...	0.37	0.33	0.45	5	485	7	0	6	1	10

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

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