CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	Alterna		RNAalifold(seed)
MCC	0.668	>	0.570
Average MCC ± 95% Confidence Intervals	0.698 ± 0.147	>	0.490 ± 0.222
Sensitivity	0.562	>	0.404
Positive Predictive Value	0.802	<	0.812
Total TP	150	>	108
Total TN	21604	<	21658
Total FP	38	>	26
Total FP CONTRA	4	<	5
Total FP INCONS	33	>	20
Total FP COMP	1	=	1
Total FN	117	<	159
P-value	0.0

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

Total Scores
MCC	0.668
Average MCC ± 95% Confidence Intervals	0.698 ± 0.147
Sensitivity	0.562
Positive Predictive Value	0.802
Nr of predictions	9

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2KDQ_B	mir-TAR links to Rfam database...	0.95	0.91	1.00	10	396	0	0	0	0	1
2KX8_A	7SK links to Rfam database...	0.88	0.83	0.94	15	845	1	0	1	0	3
2LC8_A	GP_knot1 links to Rfam database...	0.46	0.40	0.53	8	1525	7	0	7	0	12
3A3A_A	tRNA-Sec links to Rfam database...	0.84	0.70	1.00	26	3629	0	0	0	0	11
3GX2_A	SAM links to Rfam database...	0.47	0.40	0.57	16	4343	13	1	11	1	24
3IVN_B	Purine links to Rfam database...	0.74	0.61	0.90	19	2325	2	1	1	0	12
3LA5_A	Purine links to Rfam database...	0.78	0.62	1.00	21	2464	0	0	0	0	13
3RKF_A	Purine links to Rfam database...	0.69	0.56	0.86	19	2189	3	1	2	0	15
3SD1_A	THF links to Rfam database...	0.46	0.38	0.57	16	3888	12	1	11	0	26

Total Scores
MCC	0.570
Average MCC ± 95% Confidence Intervals	0.490 ± 0.222
Sensitivity	0.404
Positive Predictive Value	0.812
Nr of predictions	9

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2KDQ_B	mir-TAR links to Rfam database...	0.52	0.27	1.00	3	403	0	0	0	0	8
2KX8_A	7SK links to Rfam database...	0.00	0.00	0.00	0	861	0	0	0	0	18
2LC8_A	GP_knot1 links to Rfam database...	-0.01	0.00	0.00	0	1528	12	0	12	0	20
3A3A_A	tRNA-Sec links to Rfam database...	0.71	0.51	1.00	19	3636	0	0	0	0	18
3GX2_A	SAM links to Rfam database...	0.74	0.55	1.00	22	4349	1	0	0	1	18
3IVN_B	Purine links to Rfam database...	0.61	0.48	0.79	15	2327	4	2	2	0	16
3LA5_A	Purine links to Rfam database...	0.63	0.47	0.84	16	2466	3	1	2	0	18
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

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