CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	Multilign(seed)		MCFold
MCC	0.574	>	0.476
Average MCC ± 95% Confidence Intervals	0.545 ± 0.313	>	0.505 ± 0.283
Sensitivity	0.524	>	0.508
Positive Predictive Value	0.638	>	0.459
Total TP	97	>	94
Total TN	14178	>	14125
Total FP	56	<	130
Total FP CONTRA	19	<	21
Total FP INCONS	36	<	90
Total FP COMP	1	<	19
Total FN	88	<	91
P-value	0.0

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

Total Scores
MCC	0.574
Average MCC ± 95% Confidence Intervals	0.545 ± 0.313
Sensitivity	0.524
Positive Predictive Value	0.638
Nr of predictions	8

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2L94_A	HIV_FE links to Rfam database...	0.97	0.94	1.00	17	340	0	0	0	0	1
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
3ZEX_C	5_8S_rRNA links to Rfam database...	0.50	0.45	0.57	13	5351	11	3	7	1	16
4FRN_A	AdoCbl-variant links to Rfam database...	0.27	0.21	0.35	6	1831	11	2	9	0	22
4JF2_A	preQ1-II links to Rfam database...	0.89	0.79	1.00	19	1063	0	0	0	0	5

Total Scores
MCC	0.476
Average MCC ± 95% Confidence Intervals	0.505 ± 0.283
Sensitivity	0.508
Positive Predictive Value	0.459
Nr of predictions	8

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2L94_A	HIV_FE links to Rfam database...	1.00	1.00	1.00	18	339	1	0	0	1	0
2LC8_A	GP_knot1 links to Rfam database...	0.44	0.44	0.47	8	511	10	0	9	1	10
3J3E_8	5_8S_rRNA links to Rfam database...	0.15	0.20	0.12	3	2716	36	11	12	13	12
3RKF_A	Purine links to Rfam database...	0.89	0.88	0.91	21	843	3	0	2	1	3
3SD1_A	THF links to Rfam database...	0.43	0.45	0.43	13	1503	17	1	16	0	16
3ZEX_C	5_8S_rRNA links to Rfam database...	0.30	0.34	0.27	10	5337	28	6	21	1	19
4FRN_A	AdoCbl-variant links to Rfam database...	0.09	0.11	0.10	3	1818	28	2	25	1	25
4JF2_A	preQ1-II links to Rfam database...	0.74	0.75	0.75	18	1058	7	1	5	1	6

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