CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	Multilign(seed)		RNASLOpt
MCC	0.533	>	0.458
Average MCC ± 95% Confidence Intervals	0.481 ± 0.286	>	0.455 ± 0.271
Sensitivity	0.411	>	0.366
Positive Predictive Value	0.698	>	0.578
Total TP	120	>	107
Total TN	44378	>	44365
Total FP	54	<	102
Total FP CONTRA	11	>	8
Total FP INCONS	41	<	70
Total FP COMP	2	<	24
Total FN	172	<	185
P-value	0.0

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

Total Scores
MCC	0.533
Average MCC ± 95% Confidence Intervals	0.481 ± 0.286
Sensitivity	0.411
Positive Predictive Value	0.698
Nr of predictions	8

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
3W1K_J	tRNA-Sec links to Rfam database...	0.87	0.79	0.97	30	4155	1	1	0	0	8
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
4AOB_A	SAM links to Rfam database...	0.61	0.45	0.83	19	4348	5	0	4	1	23
4FRN_A	AdoCbl-variant links to Rfam database...	0.24	0.17	0.35	6	5134	11	1	10	0	30
4JF2_A	preQ1-II links to Rfam database...	0.78	0.61	1.00	19	2831	0	0	0	0	12

Total Scores
MCC	0.458
Average MCC ± 95% Confidence Intervals	0.455 ± 0.271
Sensitivity	0.366
Positive Predictive Value	0.578
Nr of predictions	8

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...	0.47	0.35	0.64	7	1529	4	0	4	0	13
3J3E_8	5_8S_rRNA links to Rfam database...	0.00	0.00	0.00	0	7483	30	1	19	10	33
3W1K_J	tRNA-Sec links to Rfam database...	0.84	0.74	0.97	28	4157	1	1	0	0	10
3W3S_B	tRNA-Sec links to Rfam database...	0.82	0.70	0.97	28	4724	2	0	1	1	12
3ZEX_C	5_8S_rRNA links to Rfam database...	0.26	0.21	0.33	11	14163	35	2	20	13	41
4AOB_A	SAM links to Rfam database...	0.26	0.19	0.38	8	4350	13	2	11	0	34
4FRN_A	AdoCbl-variant links to Rfam database...	0.20	0.17	0.26	6	5128	17	2	15	0	30
4JF2_A	preQ1-II links to Rfam database...	0.78	0.61	1.00	19	2831	0	0	0	0	12

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