CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	RNASampler(seed)		RSpredict(20)
MCC	0.570	>	0.502
Average MCC ± 95% Confidence Intervals	0.606 ± 0.218	>	0.552 ± 0.256
Sensitivity	0.434	<	0.461
Positive Predictive Value	0.754	>	0.552
Total TP	95	<	101
Total TN	45183	>	45126
Total FP	46	<	100
Total FP CONTRA	4	<	24
Total FP INCONS	27	<	58
Total FP COMP	15	<	18
Total FN	124	>	118
P-value	0.0

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

Total Scores
MCC	0.570
Average MCC ± 95% Confidence Intervals	0.606 ± 0.218
Sensitivity	0.434
Positive Predictive Value	0.754
Nr of predictions	7

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
3IVN_B	Purine links to Rfam database...	0.78	0.61	1.00	19	2327	0	0	0	0	12
3JYX_4	5_8S_rRNA links to Rfam database...	0.39	0.30	0.50	10	12226	13	2	8	3	23
3O58_3	5_8S_rRNA links to Rfam database...	0.45	0.34	0.60	12	12383	12	2	6	4	23
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...	0.60	0.38	0.94	16	3899	1	0	1	0	26
4A1C_2	5_8S_rRNA links to Rfam database...	0.31	0.24	0.40	8	11761	20	0	12	8	25

Total Scores
MCC	0.502
Average MCC ± 95% Confidence Intervals	0.552 ± 0.256
Sensitivity	0.461
Positive Predictive Value	0.552
Nr of predictions	7

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...	0.85	0.73	1.00	8	398	0	0	0	0	3
3IVN_B	Purine links to Rfam database...	0.78	0.65	0.95	20	2325	1	0	1	0	11
3JYX_4	5_8S_rRNA links to Rfam database...	0.28	0.27	0.30	9	12216	33	5	16	12	24
3O58_3	5_8S_rRNA links to Rfam database...	0.32	0.34	0.30	12	12363	28	12	16	0	23
3RKF_A	Purine links to Rfam database...	0.77	0.62	0.95	21	2189	1	0	1	0	13
3SD1_A	THF links to Rfam database...	0.68	0.60	0.78	25	3884	7	1	6	0	17
4A1C_2	5_8S_rRNA links to Rfam database...	0.19	0.18	0.20	6	11751	30	6	18	6	27

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