CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	Multilign(20)		RSpredict(seed)
MCC	0.612	>	0.349
Average MCC ± 95% Confidence Intervals	0.608 ± 0.232	>	0.283 ± 0.205
Sensitivity	0.581	>	0.191
Positive Predictive Value	0.657	>	0.657
Total TP	140	>	46
Total TN	15429	<	15572
Total FP	88	>	26
Total FP CONTRA	19	>	5
Total FP INCONS	54	>	19
Total FP COMP	15	>	2
Total FN	101	<	195
P-value	1.69265863073e-08

Comparison of performance of Multilign(20) and RSpredict(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(20) and RSpredict(seed)).
Comparison of average Matthews Correlation Coefficients (MCCs) for Multilign(20) and RSpredict(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(20) and RSpredict(seed)).

Total Scores
MCC	0.612
Average MCC ± 95% Confidence Intervals	0.608 ± 0.232
Sensitivity	0.581
Positive Predictive Value	0.657
Nr of predictions	10

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
2XXA_G	Bacteria_small_SRP links to Rfam database...	-0.01	0.00	0.00	0	2033	12	2	10	0	35
3AMU_B	tRNA links to Rfam database...	0.71	0.74	0.70	14	1137	9	0	6	3	5
3RKF_A	Purine links to Rfam database...	0.91	0.88	0.95	21	844	1	0	1	0	3
3SD1_A	THF links to Rfam database...	0.68	0.69	0.69	20	1504	9	4	5	0	9
4A1C_3	5S_rRNA links to Rfam database...	0.88	0.86	0.89	32	2727	6	0	4	2	5
4A1C_2	5_8S_rRNA links to Rfam database...	0.20	0.25	0.16	5	4485	33	9	17	7	15
4AOB_A	SAM links to Rfam database...	0.59	0.55	0.64	16	1412	10	3	6	1	13
4ENB_A	crcB links to Rfam database...	0.39	0.33	0.50	5	462	6	0	5	1	10
4ENC_A	crcB links to Rfam database...	0.73	0.60	0.90	9	486	1	1	0	0	6

Total Scores
MCC	0.349
Average MCC ± 95% Confidence Intervals	0.283 ± 0.205
Sensitivity	0.191
Positive Predictive Value	0.657
Nr of predictions	10

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...	0.55	0.50	0.64	9	343	6	0	5	1	9
2XXA_G	Bacteria_small_SRP links to Rfam database...	0.37	0.20	0.70	7	2035	3	0	3	0	28
3AMU_B	tRNA links to Rfam database...	-0.01	0.00	0.00	0	1155	2	0	2	0	19
3RKF_A	Purine links to Rfam database...	0.84	0.75	0.95	18	847	1	1	0	0	6
3SD1_A	THF links to Rfam database...	0.00	0.00	0.00	0	1533	0	0	0	0	29
4A1C_3	5S_rRNA links to Rfam database...	0.00	0.00	0.00	0	2759	4	2	2	0	37
4A1C_2	5_8S_rRNA links to Rfam database...	0.00	0.00	0.00	0	4512	5	2	2	1	20
4AOB_A	SAM links to Rfam database...	0.42	0.21	0.86	6	1430	1	0	1	0	23
4ENB_A	crcB links to Rfam database...	0.34	0.20	0.60	3	467	2	0	2	0	12
4ENC_A	crcB links to Rfam database...	0.34	0.20	0.60	3	491	2	0	2	0	12

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