CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	Cylofold		MCFold
MCC	0.678	>	0.512
Average MCC ± 95% Confidence Intervals	0.667 ± 0.148	>	0.478 ± 0.142
Sensitivity	0.659	>	0.543
Positive Predictive Value	0.706	>	0.497
Total TP	209	>	172
Total TN	20658	>	20608
Total FP	101	<	206
Total FP CONTRA	33	=	33
Total FP INCONS	54	<	141
Total FP COMP	14	<	32
Total FN	108	<	145
P-value	2.30549897711e-08

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

Total Scores
MCC	0.678
Average MCC ± 95% Confidence Intervals	0.667 ± 0.148
Sensitivity	0.659
Positive Predictive Value	0.706
Nr of predictions	15

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
2M58_A	-	0.60	0.58	0.64	7	533	4	1	3	0	5
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
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

Total Scores
MCC	0.512
Average MCC ± 95% Confidence Intervals	0.478 ± 0.142
Sensitivity	0.543
Positive Predictive Value	0.497
Nr of predictions	15

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...	0.44	0.44	0.47	8	511	10	0	9	1	10
2M58_A	-	0.22	0.25	0.23	3	531	13	1	9	3	9
3J0L_a	-	0.14	0.18	0.15	2	398	13	1	10	2	9
3J20_0	tRNA links to Rfam database...	0.66	0.71	0.63	15	1195	11	3	6	2	6
3NKB_B	-	0.68	0.74	0.64	14	713	8	2	6	0	5
3O58_3	5_8S_rRNA links to Rfam database...	0.28	0.36	0.22	8	4727	39	14	15	10	14
3PDR_A	ykoK links to Rfam database...	0.78	0.80	0.77	40	4788	14	5	7	2	10
3RKF_A	Purine links to Rfam database...	0.89	0.88	0.91	21	843	3	0	2	1	3
3SD1_A	THF links to Rfam database...	0.43	0.45	0.43	13	1503	17	1	16	0	16
3U4M_B	-	0.74	0.77	0.71	17	1252	10	1	6	3	5
4ATO_G	-	0.36	0.43	0.33	3	211	8	0	6	2	4
4ENB_A	crcB links to Rfam database...	0.78	0.73	0.85	11	459	4	0	2	2	4
4ENC_A	crcB links to Rfam database...	0.34	0.33	0.38	5	483	11	0	8	3	10
4FRG_B	AdoCbl-variant links to Rfam database...	0.35	0.38	0.35	9	1176	17	3	14	0	15
4FRN_A	AdoCbl-variant links to Rfam database...	0.09	0.11	0.10	3	1818	28	2	25	1	25

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