CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	RNAfold		Multilign(20)
MCC	0.603	>	0.581
Average MCC ± 95% Confidence Intervals	0.615 ± 0.300	>	0.583 ± 0.267
Sensitivity	0.606	>	0.576
Positive Predictive Value	0.611	>	0.598
Total TP	80	>	76
Total TN	9189	<	9193
Total FP	69	>	60
Total FP CONTRA	19	>	17
Total FP INCONS	32	<	34
Total FP COMP	18	>	9
Total FN	52	<	56
P-value	0.0

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

Total Scores
MCC	0.603
Average MCC ± 95% Confidence Intervals	0.615 ± 0.300
Sensitivity	0.606
Positive Predictive Value	0.611
Nr of predictions	6

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
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...	0.77	0.76	0.79	22	1505	6	4	2	0	7
4A1C_2	5_8S_rRNA links to Rfam database...	0.19	0.25	0.15	5	4482	43	11	18	14	15
4AOB_A	SAM links to Rfam database...	0.60	0.59	0.63	17	1410	11	4	6	1	12
4ENB_A	crcB links to Rfam database...	0.85	0.73	1.00	11	461	2	0	0	2	4
4ENC_A	crcB links to Rfam database...	0.37	0.33	0.45	5	485	7	0	6	1	10

Total Scores
MCC	0.581
Average MCC ± 95% Confidence Intervals	0.583 ± 0.267
Sensitivity	0.576
Positive Predictive Value	0.598
Nr of predictions	6

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
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_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

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