CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	Fold		Carnac(seed)
MCC	0.589	>	0.124
Average MCC ± 95% Confidence Intervals	0.516 ± 0.226	>	0.047 ± 0.105
Sensitivity	0.602	>	0.015
Positive Predictive Value	0.586	<	1.000
Total TP	156	>	4
Total TN	21464	<	21726
Total FP	150	>	0
Total FP CONTRA	32	>	0
Total FP INCONS	78	>	0
Total FP COMP	40	>	0
Total FN	103	<	255
P-value	1.34193807955e-08

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

Total Scores
MCC	0.589
Average MCC ± 95% Confidence Intervals	0.516 ± 0.226
Sensitivity	0.602
Positive Predictive Value	0.586
Nr of predictions	10

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
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	0.124
Average MCC ± 95% Confidence Intervals	0.047 ± 0.105
Sensitivity	0.015
Positive Predictive Value	1.000
Nr of predictions	10

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...	0.47	0.22	1.00	4	524	0	0	0	0	14
3NPB_A	SAM links to Rfam database...	0.00	0.00	0.00	0	2278	0	0	0	0	37
3O58_3	5_8S_rRNA links to Rfam database...	0.00	0.00	0.00	0	4764	0	0	0	0	22
3PDR_A	ykoK links to Rfam database...	0.00	0.00	0.00	0	4840	0	0	0	0	50
3RKF_A	Purine links to Rfam database...	0.00	0.00	0.00	0	866	0	0	0	0	24
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	4516	0	0	0	0	20
4AOB_A	SAM links to Rfam database...	0.00	0.00	0.00	0	1437	0	0	0	0	29
4ENB_A	crcB links to Rfam database...	0.00	0.00	0.00	0	472	0	0	0	0	15
4ENC_A	crcB links to Rfam database...	0.00	0.00	0.00	0	496	0	0	0	0	15

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