CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	RNAalifold(seed)		IPknot
MCC	0.523	>	0.505
Average MCC ± 95% Confidence Intervals	0.490 ± 0.224	<	0.521 ± 0.198
Sensitivity	0.344	<	0.402
Positive Predictive Value	0.800	>	0.641
Total TP	72	<	84
Total TN	26330	>	26289
Total FP	21	<	53
Total FP CONTRA	2	<	6
Total FP INCONS	16	<	41
Total FP COMP	3	<	6
Total FN	137	>	125
P-value	0.0

Comparison of performance of RNAalifold(seed) and IPknot. 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 RNAalifold(seed) and IPknot).
Comparison of average Matthews Correlation Coefficients (MCCs) for RNAalifold(seed) and IPknot. 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 RNAalifold(seed) and IPknot).

Total Scores
MCC	0.523
Average MCC ± 95% Confidence Intervals	0.490 ± 0.224
Sensitivity	0.344
Positive Predictive Value	0.800
Nr of predictions	7

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	1528	12	0	12	0	20
3RKF_A	Purine links to Rfam database...	0.63	0.47	0.84	16	2192	3	1	2	0	18
3SD1_A	THF links to Rfam database...	0.58	0.40	0.85	17	3896	3	1	2	0	25
4A1C_2	5_8S_rRNA links to Rfam database...	0.39	0.15	1.00	5	11776	2	0	0	2	28
4AOB_A	SAM links to Rfam database...	0.72	0.52	1.00	22	4349	1	0	0	1	20
4ENB_A	crcB links to Rfam database...	0.56	0.32	1.00	6	1269	0	0	0	0	13
4ENC_A	crcB links to Rfam database...	0.56	0.32	1.00	6	1320	0	0	0	0	13

Total Scores
MCC	0.505
Average MCC ± 95% Confidence Intervals	0.521 ± 0.198
Sensitivity	0.402
Positive Predictive Value	0.641
Nr of predictions	7

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...	0.40	0.30	0.55	6	1529	5	1	4	0	14
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...	0.61	0.48	0.80	20	3891	5	0	5	0	22
4A1C_2	5_8S_rRNA links to Rfam database...	0.17	0.15	0.19	5	11755	26	4	17	5	28
4AOB_A	SAM links to Rfam database...	0.42	0.33	0.54	14	4345	13	1	11	1	28
4ENB_A	crcB links to Rfam database...	0.76	0.58	1.00	11	1264	0	0	0	0	8
4ENC_A	crcB links to Rfam database...	0.52	0.42	0.67	8	1314	4	0	4	0	11

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