CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	Multilign(seed)		Pknots
MCC	0.556	>	0.501
Average MCC ± 95% Confidence Intervals	0.517 ± 0.225	<	0.541 ± 0.229
Sensitivity	0.432	<	0.446
Positive Predictive Value	0.723	>	0.569
Total TP	159	<	164
Total TN	50457	>	50389
Total FP	63	<	140
Total FP CONTRA	12	<	13
Total FP INCONS	49	<	111
Total FP COMP	2	<	16
Total FN	209	>	204
P-value	5.9854753845e-09

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

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	0.501
Average MCC ± 95% Confidence Intervals	0.541 ± 0.229
Sensitivity	0.446
Positive Predictive Value	0.569
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...	0.79	0.75	0.83	15	1522	3	1	2	0	5
3J3E_8	5_8S_rRNA links to Rfam database...	0.07	0.06	0.08	2	7479	33	2	20	11	31
3RKF_A	Purine links to Rfam database...	0.77	0.62	0.95	21	2189	1	0	1	0	13
3SD1_A	THF links to Rfam database...	0.65	0.52	0.81	22	3889	5	0	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...	0.71	0.63	0.81	25	4722	7	0	6	1	15
3ZEX_C	5_8S_rRNA links to Rfam database...	0.07	0.08	0.07	4	14141	54	4	47	3	48
4AOB_A	SAM links to Rfam database...	0.17	0.14	0.21	6	4343	23	1	21	1	36
4FRN_A	AdoCbl-variant links to Rfam database...	0.51	0.42	0.63	15	5127	9	1	8	0	21
4JF2_A	preQ1-II links to Rfam database...	0.81	0.77	0.86	24	2822	4	3	1	0	7

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