CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	Afold		Cylofold
MCC	0.679	>	0.673
Average MCC ± 95% Confidence Intervals	0.686 ± 0.172	>	0.680 ± 0.219
Sensitivity	0.699	>	0.680
Positive Predictive Value	0.669	<	0.675
Total TP	107	>	104
Total TN	10300	<	10306
Total FP	74	>	60
Total FP CONTRA	9	<	13
Total FP INCONS	44	>	37
Total FP COMP	21	>	10
Total FN	46	<	49
P-value	0.0

Comparison of performance of Afold and Cylofold. 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 Afold and Cylofold).
Comparison of average Matthews Correlation Coefficients (MCCs) for Afold and Cylofold. 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 Afold and Cylofold).

Total Scores
MCC	0.679
Average MCC ± 95% Confidence Intervals	0.686 ± 0.172
Sensitivity	0.699
Positive Predictive Value	0.669
Nr of predictions	7

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...	0.64	0.61	0.69	11	512	6	0	5	1	7
3ADB_C	-	0.85	0.85	0.85	28	1786	6	0	5	1	5
3NKB_B	-	0.69	0.74	0.67	14	714	7	0	7	0	5
3O58_3	5_8S_rRNA links to Rfam database...	0.41	0.50	0.34	11	4732	38	6	15	17	11
3RKF_A	Purine links to Rfam database...	0.91	0.83	1.00	20	846	0	0	0	0	4
3U4M_B	-	0.49	0.55	0.46	12	1250	14	3	11	0	10
4ENB_A	crcB links to Rfam database...	0.81	0.73	0.92	11	460	3	0	1	2	4

Total Scores
MCC	0.673
Average MCC ± 95% Confidence Intervals	0.680 ± 0.219
Sensitivity	0.680
Positive Predictive Value	0.675
Nr of predictions	7

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...	0.64	0.61	0.69	11	512	5	1	4	0	7
3ADB_C	-	0.84	0.82	0.87	27	1788	4	0	4	0	6
3NKB_B	-	0.46	0.42	0.53	8	720	7	0	7	0	11
3O58_3	5_8S_rRNA links to Rfam database...	0.42	0.50	0.35	11	4733	30	9	11	10	11
3RKF_A	Purine links to Rfam database...	0.91	0.83	1.00	20	846	0	0	0	0	4
3U4M_B	-	0.49	0.55	0.46	12	1250	14	3	11	0	10
4ENB_A	crcB links to Rfam database...	1.00	1.00	1.00	15	457	0	0	0	0	0

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