CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	Multilign(seed)		RNAshapes
MCC	0.556	>	0.540
Average MCC ± 95% Confidence Intervals	0.517 ± 0.225	<	0.563 ± 0.163
Sensitivity	0.432	<	0.462
Positive Predictive Value	0.723	>	0.637
Total TP	159	<	170
Total TN	50457	>	50410
Total FP	63	<	115
Total FP CONTRA	12	>	10
Total FP INCONS	49	<	87
Total FP COMP	2	<	18
Total FN	209	>	198
P-value	0.00137673878406

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

Total Scores
MCC	0.556
Average MCC ± 95% Confidence Intervals	0.517 ± 0.225
Sensitivity	0.432
Positive Predictive Value	0.723
Nr of predictions	10

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
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	0.540
Average MCC ± 95% Confidence Intervals	0.563 ± 0.163
Sensitivity	0.462
Positive Predictive Value	0.637
Nr of predictions	10

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...	0.61	0.55	0.69	11	1524	5	0	5	0	9
3J3E_8	5_8S_rRNA links to Rfam database...	0.17	0.15	0.19	5	7477	29	2	19	8	28
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...	0.64	0.52	0.79	22	3888	6	1	5	0	20
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...	0.55	0.48	0.63	19	4723	12	1	10	1	21
3ZEX_C	5_8S_rRNA links to Rfam database...	0.23	0.21	0.25	11	14152	41	1	32	8	41
4AOB_A	SAM links to Rfam database...	0.50	0.40	0.63	17	4344	11	2	8	1	25
4FRN_A	AdoCbl-variant links to Rfam database...	0.52	0.44	0.62	16	5125	10	2	8	0	20
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.