CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	ContextFold		Multilign(20)
MCC	0.706	>	0.557
Average MCC ± 95% Confidence Intervals	0.694 ± 0.149	>	0.541 ± 0.192
Sensitivity	0.565	>	0.472
Positive Predictive Value	0.885	>	0.663
Total TP	200	>	167
Total TN	49825	>	49799
Total FP	43	<	93
Total FP CONTRA	3	<	8
Total FP INCONS	23	<	77
Total FP COMP	17	>	8
Total FN	154	<	187
P-value	1.12262428713e-08

Comparison of performance of ContextFold 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 ContextFold and Multilign(20)).
Average Matthews Correlation Coefficients (MCC) with 95% confidence intervals (CIs) were plotted for different RNA families, for which at least 3 members were present in the benchmarking dataset. 'n' denotes the number of MCCs used to calculate the average and CI. See tables below for raw data (individual counts for ContextFold and Multilign(20)).
Comparison of average Matthews Correlation Coefficients (MCCs) for ContextFold 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 ContextFold and Multilign(20)).

Total Scores
MCC	0.706
Average MCC ± 95% Confidence Intervals	0.694 ± 0.149
Sensitivity	0.565
Positive Predictive Value	0.885
Nr of predictions	10

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
3J20_0	tRNA links to Rfam database...	0.84	0.70	1.00	21	2829	1	0	0	1	9
3J20_1	tRNA links to Rfam database...	0.96	0.91	1.00	21	2905	0	0	0	0	2
3J2L_3	5S_rRNA links to Rfam database...	0.79	0.62	1.00	33	7842	2	0	0	2	20
3ZEX_D	5S_rRNA links to Rfam database...	0.81	0.67	0.97	33	6987	1	0	1	0	16
4A1C_2	5_8S_rRNA links to Rfam database...	0.20	0.15	0.28	5	11763	26	0	13	13	28
4A1C_3	5S_rRNA links to Rfam database...	0.78	0.63	0.97	34	7105	1	0	1	0	20
4AOB_A	SAM links to Rfam database...	0.52	0.40	0.68	17	4346	9	1	7	1	25
4ENB_A	crcB links to Rfam database...	0.69	0.47	1.00	9	1266	0	0	0	0	10
4ENC_A	crcB links to Rfam database...	0.65	0.47	0.90	9	1316	1	1	0	0	10
4FRG_B	AdoCbl-variant links to Rfam database...	0.71	0.56	0.90	18	3466	2	1	1	0	14

Total Scores
MCC	0.557
Average MCC ± 95% Confidence Intervals	0.541 ± 0.192
Sensitivity	0.472
Positive Predictive Value	0.663
Nr of predictions	10

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
3J20_0	tRNA links to Rfam database...	0.61	0.53	0.70	16	2827	8	1	6	1	14
3J20_1	tRNA links to Rfam database...	0.96	0.91	1.00	21	2905	0	0	0	0	2
3J2L_3	5S_rRNA links to Rfam database...	0.65	0.53	0.80	28	7840	9	0	7	2	25
3ZEX_D	5S_rRNA links to Rfam database...	0.75	0.65	0.86	32	6984	5	1	4	0	17
4A1C_2	5_8S_rRNA links to Rfam database...	0.15	0.15	0.15	5	11747	33	3	26	4	28
4A1C_3	5S_rRNA links to Rfam database...	0.70	0.59	0.84	32	7102	6	0	6	0	22
4AOB_A	SAM links to Rfam database...	0.49	0.38	0.64	16	4346	10	1	8	1	26
4ENB_A	crcB links to Rfam database...	0.34	0.26	0.45	5	1264	6	1	5	0	14
4ENC_A	crcB links to Rfam database...	0.65	0.47	0.90	9	1316	1	1	0	0	10
4FRG_B	AdoCbl-variant links to Rfam database...	0.12	0.09	0.17	3	3468	15	0	15	0	29

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