CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	ContextFold		RSpredict(seed)
MCC	0.732	>	0.131
Average MCC ± 95% Confidence Intervals	0.719 ± 0.194	>	0.130 ± 0.162
Sensitivity	0.673	>	0.070
Positive Predictive Value	0.804	>	0.267
Total TP	115	>	12
Total TN	12521	<	12619
Total FP	50	>	34
Total FP CONTRA	6	<	7
Total FP INCONS	22	<	26
Total FP COMP	22	>	1
Total FN	56	<	159
P-value	0.0

Comparison of performance of ContextFold 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 ContextFold and RSpredict(seed)).
Comparison of average Matthews Correlation Coefficients (MCCs) for ContextFold 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 ContextFold and RSpredict(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	0.131
Average MCC ± 95% Confidence Intervals	0.130 ± 0.162
Sensitivity	0.070
Positive Predictive Value	0.267
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	515	13	0	13	0	18
3J16_L	tRNA links to Rfam database...	0.00	0.00	0.00	0	1158	1	0	1	0	21
3UZL_B	tRNA links to Rfam database...	-0.01	0.00	0.00	0	1287	6	3	3	0	16
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.