CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	Multilign(seed)		RNASampler(seed)
MCC	0.534	>	0.432
Average MCC ± 95% Confidence Intervals	0.492 ± 0.310	>	0.414 ± 0.259
Sensitivity	0.413	>	0.282
Positive Predictive Value	0.698	>	0.670
Total TP	104	>	71
Total TN	36820	<	36863
Total FP	46	<	47
Total FP CONTRA	10	>	3
Total FP INCONS	35	>	32
Total FP COMP	1	<	12
Total FN	148	<	181
P-value	0.0

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

Total Scores
MCC	0.534
Average MCC ± 95% Confidence Intervals	0.492 ± 0.310
Sensitivity	0.413
Positive Predictive Value	0.698
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	1	11	0	20
3J3E_8	5_8S_rRNA links to Rfam database...	0.13	0.09	0.19	3	7487	13	5	8	0	30
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...	0.55	0.45	0.68	19	3888	9	1	8	0	23
3W3S_B	tRNA-Sec links to Rfam database...	0.84	0.73	0.97	29	4723	2	0	1	1	11
3ZEX_C	5_8S_rRNA links to Rfam database...	0.39	0.27	0.58	14	14172	10	3	7	0	38
4JF2_A	preQ1-II links to Rfam database...	0.78	0.61	1.00	19	2831	0	0	0	0	12

Total Scores
MCC	0.432
Average MCC ± 95% Confidence Intervals	0.414 ± 0.259
Sensitivity	0.282
Positive Predictive Value	0.670
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	1530	10	0	10	0	20
3J3E_8	5_8S_rRNA links to Rfam database...	0.12	0.09	0.17	3	7485	22	2	13	7	30
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
3W3S_B	tRNA-Sec links to Rfam database...	0.55	0.30	1.00	12	4741	1	0	0	1	28
3ZEX_C	5_8S_rRNA links to Rfam database...	0.32	0.19	0.53	10	14177	13	1	8	4	42
4JF2_A	preQ1-II links to Rfam database...	0.57	0.32	1.00	10	2840	0	0	0	0	21

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