CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	Fold		RSpredict(seed)
MCC	0.532	>	0.231
Average MCC ± 95% Confidence Intervals	0.500 ± 0.189	>	0.216 ± 0.162
Sensitivity	0.570	>	0.119
Positive Predictive Value	0.502	>	0.457
Total TP	231	>	48
Total TN	69246	<	69601
Total FP	292	>	66
Total FP CONTRA	88	>	15
Total FP INCONS	141	>	42
Total FP COMP	63	>	9
Total FN	174	<	357
P-value	2.41358941668e-08

Comparison of performance of Fold and RSpredict(seed). 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 Fold and RSpredict(seed)).
Comparison of average Matthews Correlation Coefficients (MCCs) for Fold and RSpredict(seed). 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 Fold and RSpredict(seed)).

Total Scores
MCC	0.532
Average MCC ± 95% Confidence Intervals	0.500 ± 0.189
Sensitivity	0.570
Positive Predictive Value	0.502
Nr of predictions	12

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
3IYQ_A	tmRNA links to Rfam database...	0.24	0.33	0.18	17	22345	95	40	38	17	34
3IZ4_A	tmRNA links to Rfam database...	0.60	0.61	0.59	58	25437	47	16	25	6	37
3NPB_A	SAM links to Rfam database...	0.77	0.73	0.82	27	2245	11	0	6	5	10
3O58_3	5_8S_rRNA links to Rfam database...	0.39	0.50	0.31	11	4728	41	9	16	16	11
3PDR_A	ykoK links to Rfam database...	0.93	0.92	0.94	46	4791	5	1	2	2	4
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...	0.68	0.69	0.69	20	1504	9	4	5	0	9
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...	0.37	0.33	0.45	5	461	7	0	6	1	10
4ENC_A	crcB links to Rfam database...	0.36	0.33	0.42	5	484	8	0	7	1	10

Total Scores
MCC	0.231
Average MCC ± 95% Confidence Intervals	0.216 ± 0.162
Sensitivity	0.119
Positive Predictive Value	0.457
Nr of predictions	12

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	515	13	0	13	0	18
3IYQ_A	tmRNA links to Rfam database...	0.16	0.10	0.26	5	22421	21	10	4	7	46
3IZ4_A	tmRNA links to Rfam database...	0.26	0.11	0.63	10	25520	7	2	4	1	85
3NPB_A	SAM links to Rfam database...	-0.01	0.00	0.00	0	2274	4	0	4	0	37
3O58_3	5_8S_rRNA links to Rfam database...	0.28	0.14	0.60	3	4759	2	0	2	0	19
3PDR_A	ykoK links to Rfam database...	0.00	0.00	0.00	0	4832	8	0	8	0	50
3RKF_A	Purine links to Rfam database...	0.84	0.75	0.95	18	847	1	1	0	0	6
3SD1_A	THF links to Rfam database...	0.00	0.00	0.00	0	1533	0	0	0	0	29
4A1C_2	5_8S_rRNA links to Rfam database...	0.00	0.00	0.00	0	4512	5	2	2	1	20
4AOB_A	SAM links to Rfam database...	0.42	0.21	0.86	6	1430	1	0	1	0	23
4ENB_A	crcB links to Rfam database...	0.34	0.20	0.60	3	467	2	0	2	0	12
4ENC_A	crcB links to Rfam database...	0.34	0.20	0.60	3	491	2	0	2	0	12

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