CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	Multilign(seed)		RNASampler(seed)
MCC	0.642	>	0.519
Average MCC ± 95% Confidence Intervals	0.577 ± 0.349	>	0.488 ± 0.300
Sensitivity	0.599	>	0.407
Positive Predictive Value	0.696	>	0.673
Total TP	103	>	70
Total TN	13966	<	14010
Total FP	47	<	48
Total FP CONTRA	17	>	7
Total FP INCONS	28	>	27
Total FP COMP	2	<	14
Total FN	69	<	102
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	0.642
Average MCC ± 95% Confidence Intervals	0.577 ± 0.349
Sensitivity	0.599
Positive Predictive Value	0.696
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...	-0.03	0.00	0.00	0	516	12	2	10	0	18
3J3E_8	5_8S_rRNA links to Rfam database...	0.19	0.20	0.19	3	2726	13	8	5	0	12
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...	0.66	0.66	0.68	19	1505	9	4	5	0	10
3W3S_B	tRNA-Sec links to Rfam database...	0.92	0.88	0.97	29	1959	2	0	1	1	4
3ZEX_C	5_8S_rRNA links to Rfam database...	0.50	0.45	0.57	13	5351	11	3	7	1	16
4JF2_A	preQ1-II links to Rfam database...	0.89	0.79	1.00	19	1063	0	0	0	0	5

Total Scores
MCC	0.519
Average MCC ± 95% Confidence Intervals	0.488 ± 0.300
Sensitivity	0.407
Positive Predictive Value	0.673
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...	-0.03	0.00	0.00	0	518	10	0	10	0	18
3J3E_8	5_8S_rRNA links to Rfam database...	0.18	0.20	0.18	3	2725	22	5	9	8	12
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
3W3S_B	tRNA-Sec links to Rfam database...	0.60	0.36	1.00	12	1977	1	0	0	1	21
3ZEX_C	5_8S_rRNA links to Rfam database...	0.39	0.31	0.50	9	5356	14	2	7	5	20
4JF2_A	preQ1-II links to Rfam database...	0.64	0.42	1.00	10	1072	0	0	0	0	14

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