CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	CentroidFold		Cylofold
MCC	0.742	>	0.669
Average MCC ± 95% Confidence Intervals	0.687 ± 0.120	>	0.663 ± 0.123
Sensitivity	0.699	>	0.648
Positive Predictive Value	0.796	>	0.700
Total TP	304	>	282
Total TN	27841	>	27820
Total FP	97	<	145
Total FP CONTRA	22	<	41
Total FP INCONS	56	<	80
Total FP COMP	19	<	24
Total FN	131	<	153
P-value	3.21671975982e-08

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

Total Scores
MCC	0.742
Average MCC ± 95% Confidence Intervals	0.687 ± 0.120
Sensitivity	0.699
Positive Predictive Value	0.796
Nr of predictions	19

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...	0.51	0.39	0.70	7	518	3	1	2	0	11
2M58_A	-	-0.02	0.00	0.00	0	538	6	0	6	0	12
3ADB_C	-	0.98	0.97	1.00	32	1787	0	0	0	0	1
3J0L_a	-	0.41	0.36	0.50	4	403	5	3	1	1	7
3J20_0	tRNA links to Rfam database...	0.54	0.57	0.52	12	1196	12	3	8	1	9
3NKB_B	-	0.66	0.68	0.65	13	715	7	0	7	0	6
3O58_3	5_8S_rRNA links to Rfam database...	0.44	0.41	0.47	9	4745	11	1	9	1	13
3PDR_A	ykoK links to Rfam database...	0.88	0.86	0.90	43	4792	7	2	3	2	7
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...	0.70	0.69	0.71	20	1505	8	4	4	0	9
3U4M_B	-	0.81	0.77	0.85	17	1256	5	0	3	2	5
3W3S_B	tRNA-Sec links to Rfam database...	0.95	0.91	1.00	30	1959	1	0	0	1	3
4AOB_A	SAM links to Rfam database...	0.50	0.48	0.54	14	1411	13	3	9	1	15
4ATO_G	-	0.61	0.57	0.67	4	214	2	0	2	0	3
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
4FRG_B	AdoCbl-variant links to Rfam database...	0.75	0.71	0.81	17	1181	4	3	1	0	7
4FRN_A	AdoCbl-variant links to Rfam database...	0.80	0.71	0.91	20	1826	2	1	1	0	8

Total Scores
MCC	0.669
Average MCC ± 95% Confidence Intervals	0.663 ± 0.123
Sensitivity	0.648
Positive Predictive Value	0.700
Nr of predictions	19

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
2M58_A	-	0.60	0.58	0.64	7	533	4	1	3	0	5
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
3J20_0	tRNA links to Rfam database...	0.74	0.76	0.73	16	1197	7	3	3	1	5
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
3W3S_B	tRNA-Sec links to Rfam database...	0.48	0.45	0.52	15	1960	15	1	13	1	18
4AOB_A	SAM links to Rfam database...	0.42	0.38	0.48	11	1414	13	3	9	1	18
4ATO_G	-	0.88	1.00	0.78	7	211	2	2	0	0	0
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
4FRG_B	AdoCbl-variant links to Rfam database...	0.93	0.88	1.00	21	1181	0	0	0	0	3
4FRN_A	AdoCbl-variant links to Rfam database...	0.23	0.18	0.31	5	1832	11	7	4	0	23

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