CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	Fold		Carnac(seed)
MCC	0.551	>	0.088
Average MCC ± 95% Confidence Intervals	0.496 ± 0.156	>	0.034 ± 0.075
Sensitivity	0.486	>	0.008
Positive Predictive Value	0.630	<	1.000
Total TP	247	>	4
Total TN	79635	<	80023
Total FP	175	>	0
Total FP CONTRA	21	>	0
Total FP INCONS	124	>	0
Total FP COMP	30	>	0
Total FN	261	<	504
P-value	1.70887622364e-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)).
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 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	0.551
Average MCC ± 95% Confidence Intervals	0.496 ± 0.156
Sensitivity	0.486
Positive Predictive Value	0.630
Nr of predictions	13

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...	-0.01	0.00	0.00	0	1525	15	2	13	0	20
3IZF_C	5S_rRNA links to Rfam database...	0.70	0.59	0.82	32	6864	7	1	6	0	22
3NPB_A	SAM links to Rfam database...	0.70	0.61	0.80	28	6986	10	1	6	3	18
3O58_2	5S_rRNA links to Rfam database...	0.71	0.71	0.71	27	7222	12	3	8	1	11
3O58_3	5_8S_rRNA links to Rfam database...	0.29	0.31	0.28	11	12363	41	3	26	12	24
3PDR_A	ykoK links to Rfam database...	0.77	0.64	0.94	46	12831	5	0	3	2	26
3RKF_A	Purine links to Rfam database...	0.76	0.59	1.00	20	2191	0	0	0	0	14
3SD1_A	THF links to Rfam database...	0.57	0.48	0.69	20	3887	9	1	8	0	22
4A1C_2	5_8S_rRNA links to Rfam database...	0.14	0.15	0.14	5	11744	43	5	27	11	28
4A1C_3	5S_rRNA links to Rfam database...	0.68	0.57	0.82	31	7102	7	1	6	0	23
4AOB_A	SAM links to Rfam database...	0.50	0.40	0.63	17	4344	11	2	8	1	25
4ENB_A	crcB links to Rfam database...	0.32	0.26	0.42	5	1263	7	1	6	0	14
4ENC_A	crcB links to Rfam database...	0.31	0.26	0.38	5	1313	8	1	7	0	14

Total Scores
MCC	0.088
Average MCC ± 95% Confidence Intervals	0.034 ± 0.075
Sensitivity	0.008
Positive Predictive Value	1.000
Nr of predictions	13

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...	0.44	0.20	1.00	4	1536	0	0	0	0	16
3IZF_C	5S_rRNA links to Rfam database...	0.00	0.00	0.00	0	6903	0	0	0	0	54
3NPB_A	SAM links to Rfam database...	0.00	0.00	0.00	0	7021	0	0	0	0	46
3O58_2	5S_rRNA links to Rfam database...	0.00	0.00	0.00	0	7260	0	0	0	0	38
3O58_3	5_8S_rRNA links to Rfam database...	0.00	0.00	0.00	0	12403	0	0	0	0	35
3PDR_A	ykoK links to Rfam database...	0.00	0.00	0.00	0	12880	0	0	0	0	72
3RKF_A	Purine links to Rfam database...	0.00	0.00	0.00	0	2211	0	0	0	0	34
3SD1_A	THF links to Rfam database...	0.00	0.00	0.00	0	3916	0	0	0	0	42
4A1C_2	5_8S_rRNA links to Rfam database...	0.00	0.00	0.00	0	11781	0	0	0	0	33
4A1C_3	5S_rRNA links to Rfam database...	0.00	0.00	0.00	0	7140	0	0	0	0	54
4AOB_A	SAM links to Rfam database...	0.00	0.00	0.00	0	4371	0	0	0	0	42
4ENB_A	crcB links to Rfam database...	0.00	0.00	0.00	0	1275	0	0	0	0	19
4ENC_A	crcB links to Rfam database...	0.00	0.00	0.00	0	1326	0	0	0	0	19

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