CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	Contrafold		Cylofold
MCC	0.727	>	0.693
Average MCC ± 95% Confidence Intervals	0.711 ± 0.122	>	0.672 ± 0.157
Sensitivity	0.719	>	0.681
Positive Predictive Value	0.743	>	0.715
Total TP	223	>	211
Total TN	20901	<	20906
Total FP	94	<	106
Total FP CONTRA	29	>	27
Total FP INCONS	48	<	57
Total FP COMP	17	<	22
Total FN	87	<	99
P-value	2.02510705504e-08

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

Total Scores
MCC	0.727
Average MCC ± 95% Confidence Intervals	0.711 ± 0.122
Sensitivity	0.719
Positive Predictive Value	0.743
Nr of predictions	13

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2KRL_A	-	0.91	0.87	0.95	20	2003	9	1	0	8	3
2LC8_A	GP_knot1 links to Rfam database...	0.46	0.39	0.58	7	516	5	3	2	0	11
3ADB_C	-	0.98	0.97	1.00	32	1787	0	0	0	0	1
3J0L_a	-	0.53	0.55	0.55	6	400	6	3	2	1	5
3NKB_B	-	0.63	0.68	0.59	13	713	9	0	9	0	6
3O58_3	5_8S_rRNA links to Rfam database...	0.32	0.36	0.29	8	4736	21	7	13	1	14
3PDR_A	ykoK links to Rfam database...	0.83	0.86	0.80	43	4786	13	5	6	2	7
3RKF_A	Purine links to Rfam database...	0.87	0.83	0.91	20	844	2	2	0	0	4
3SD1_A	THF links to Rfam database...	0.68	0.69	0.69	20	1504	9	5	4	0	9
3U4M_B	-	0.81	0.77	0.85	17	1256	5	0	3	2	5
4AOB_A	SAM links to Rfam database...	0.53	0.52	0.56	15	1410	13	3	9	1	14
4ENB_A	crcB links to Rfam database...	0.85	0.73	1.00	11	461	1	0	0	1	4
4ENC_A	crcB links to Rfam database...	0.85	0.73	1.00	11	485	1	0	0	1	4

Total Scores
MCC	0.693
Average MCC ± 95% Confidence Intervals	0.672 ± 0.157
Sensitivity	0.681
Positive Predictive Value	0.715
Nr of predictions	13

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2KRL_A	-	0.85	0.87	0.83	20	2000	12	4	0	8	3
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
3J0L_a	-	0.17	0.18	0.20	2	401	9	3	5	1	9
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
3PDR_A	ykoK links to Rfam database...	0.86	0.78	0.95	39	4799	4	1	1	2	11
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...	0.71	0.69	0.74	20	1506	7	2	5	0	9
3U4M_B	-	0.49	0.55	0.46	12	1250	14	3	11	0	10
4AOB_A	SAM links to Rfam database...	0.42	0.38	0.48	11	1414	13	3	9	1	18
4ENB_A	crcB links to Rfam database...	1.00	1.00	1.00	15	457	0	0	0	0	0
4ENC_A	crcB links to Rfam database...	0.97	1.00	0.94	15	480	1	1	0	0	0

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