CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	RNASampler(seed)		RNAalifold(20)
MCC	0.715	>	0.636
Average MCC ± 95% Confidence Intervals	0.733 ± 0.169	>	0.632 ± 0.195
Sensitivity	0.658	>	0.608
Positive Predictive Value	0.782	>	0.671
Total TP	104	>	96
Total TN	17736	>	17726
Total FP	49	<	62
Total FP CONTRA	15	<	16
Total FP INCONS	14	<	31
Total FP COMP	20	>	15
Total FN	54	<	62
P-value	0.0

Comparison of performance of RNASampler(seed) and RNAalifold(20). 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 RNASampler(seed) and RNAalifold(20)).
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 RNASampler(seed) and RNAalifold(20)).
Comparison of average Matthews Correlation Coefficients (MCCs) for RNASampler(seed) and RNAalifold(20). 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 RNASampler(seed) and RNAalifold(20)).

Total Scores
MCC	0.715
Average MCC ± 95% Confidence Intervals	0.733 ± 0.169
Sensitivity	0.658
Positive Predictive Value	0.782
Nr of predictions	8

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...	1.00	1.00	1.00	10	164	0	0	0	0	0
2L94_A	HIV_FE links to Rfam database...	0.70	0.56	0.91	10	346	2	0	1	1	8
3IVN_B	Purine links to Rfam database...	0.91	0.83	1.00	19	884	0	0	0	0	4
3JYX_4	5_8S_rRNA links to Rfam database...	0.70	0.83	0.59	10	4739	13	6	1	6	2
3O58_3	5_8S_rRNA links to Rfam database...	0.54	0.50	0.58	11	4745	13	5	3	5	11
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...	0.72	0.55	0.94	16	1516	1	0	1	0	13
4A1C_2	5_8S_rRNA links to Rfam database...	0.40	0.40	0.40	8	4496	20	4	8	8	12

Total Scores
MCC	0.636
Average MCC ± 95% Confidence Intervals	0.632 ± 0.195
Sensitivity	0.608
Positive Predictive Value	0.671
Nr of predictions	8

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...	0.62	0.40	1.00	4	170	0	0	0	0	6
2L94_A	HIV_FE links to Rfam database...	0.51	0.50	0.56	9	341	8	0	7	1	9
3IVN_B	Purine links to Rfam database...	0.86	0.78	0.95	18	884	1	1	0	0	5
3JYX_4	5_8S_rRNA links to Rfam database...	0.77	0.83	0.71	10	4742	15	3	1	11	2
3O58_3	5_8S_rRNA links to Rfam database...	0.42	0.36	0.50	8	4748	9	3	5	1	14
3RKF_A	Purine links to Rfam database...	0.81	0.71	0.94	17	848	1	0	1	0	7
3SD1_A	THF links to Rfam database...	0.84	0.86	0.83	25	1503	5	4	1	0	4
4A1C_2	5_8S_rRNA links to Rfam database...	0.22	0.25	0.19	5	4490	23	5	16	2	15

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