CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	ContextFold		MXScarna(seed)
MCC	0.732	>	0.679
Average MCC ± 95% Confidence Intervals	0.719 ± 0.194	>	0.608 ± 0.272
Sensitivity	0.673	>	0.620
Positive Predictive Value	0.804	>	0.752
Total TP	115	>	106
Total TN	12521	<	12523
Total FP	50	<	62
Total FP CONTRA	6	<	7
Total FP INCONS	22	<	28
Total FP COMP	22	<	27
Total FN	56	<	65
P-value	0.0

Comparison of performance of ContextFold and MXScarna(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 ContextFold and MXScarna(seed)).
Comparison of average Matthews Correlation Coefficients (MCCs) for ContextFold and MXScarna(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 ContextFold and MXScarna(seed)).

Total Scores
MCC	0.732
Average MCC ± 95% Confidence Intervals	0.719 ± 0.194
Sensitivity	0.673
Positive Predictive Value	0.804
Nr of predictions	8

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...	0.58	0.56	0.63	10	512	6	0	6	0	8
3J16_L	tRNA links to Rfam database...	0.90	0.81	1.00	17	1142	0	0	0	0	4
3UZL_B	tRNA links to Rfam database...	0.93	0.88	1.00	14	1279	7	0	0	7	2
4A1C_3	5S_rRNA links to Rfam database...	0.96	0.92	1.00	34	2729	1	0	0	1	3
4A1C_2	5_8S_rRNA links to Rfam database...	0.26	0.25	0.28	5	4498	26	3	10	13	15
4AOB_A	SAM links to Rfam database...	0.62	0.59	0.68	17	1412	9	2	6	1	12
4ENB_A	crcB links to Rfam database...	0.77	0.60	1.00	9	463	0	0	0	0	6
4ENC_A	crcB links to Rfam database...	0.73	0.60	0.90	9	486	1	1	0	0	6

Total Scores
MCC	0.679
Average MCC ± 95% Confidence Intervals	0.608 ± 0.272
Sensitivity	0.620
Positive Predictive Value	0.752
Nr of predictions	8

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...	-0.03	0.00	0.00	0	518	12	0	10	2	18
3J16_L	tRNA links to Rfam database...	0.98	0.95	1.00	20	1139	0	0	0	0	1
3UZL_B	tRNA links to Rfam database...	0.83	0.75	0.92	12	1280	8	0	1	7	4
4A1C_3	5S_rRNA links to Rfam database...	0.92	0.92	0.92	34	2726	6	0	3	3	3
4A1C_2	5_8S_rRNA links to Rfam database...	0.45	0.40	0.50	8	4500	20	4	4	12	12
4AOB_A	SAM links to Rfam database...	0.71	0.69	0.74	20	1410	10	2	5	3	9
4ENB_A	crcB links to Rfam database...	0.54	0.40	0.75	6	464	2	0	2	0	9
4ENC_A	crcB links to Rfam database...	0.48	0.40	0.60	6	486	4	1	3	0	9

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