CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	Multilign(seed)		RNAalifold(seed)
MCC	0.649	>	0.641
Average MCC ± 95% Confidence Intervals	0.617 ± 0.295	>	0.603 ± 0.233
Sensitivity	0.591	>	0.500
Positive Predictive Value	0.724	<	0.832
Total TP	123	>	104
Total TN	13762	<	13807
Total FP	50	>	28
Total FP CONTRA	12	>	4
Total FP INCONS	35	>	17
Total FP COMP	3	<	7
Total FN	85	<	104
P-value	0.0

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

Total Scores
MCC	0.649
Average MCC ± 95% Confidence Intervals	0.617 ± 0.295
Sensitivity	0.591
Positive Predictive Value	0.724
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
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
4AOB_A	SAM links to Rfam database...	0.73	0.66	0.83	19	1414	5	1	3	1	10
4FRN_A	AdoCbl-variant links to Rfam database...	0.27	0.21	0.35	6	1831	11	2	9	0	22

Total Scores
MCC	0.641
Average MCC ± 95% Confidence Intervals	0.603 ± 0.233
Sensitivity	0.500
Positive Predictive Value	0.832
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...	0.57	0.39	0.88	7	349	2	0	1	1	11
2LC8_A	GP_knot1 links to Rfam database...	-0.03	0.00	0.00	0	516	12	0	12	0	18
3RKF_A	Purine links to Rfam database...	0.74	0.67	0.84	16	847	3	1	2	0	8
3SD1_A	THF links to Rfam database...	0.70	0.59	0.85	17	1513	3	2	1	0	12
3W3S_B	tRNA-Sec links to Rfam database...	0.71	0.52	1.00	17	1972	2	0	0	2	16
3ZEX_C	5_8S_rRNA links to Rfam database...	0.49	0.24	1.00	7	5367	2	0	0	2	22
4AOB_A	SAM links to Rfam database...	0.85	0.72	1.00	21	1416	2	0	0	2	8
4FRN_A	AdoCbl-variant links to Rfam database...	0.78	0.68	0.90	19	1827	2	1	1	0	9

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