CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	Cylofold		CRWrnafold
MCC	0.526	>	0.473
Average MCC ± 95% Confidence Intervals	0.503 ± 0.158	>	0.425 ± 0.176
Sensitivity	0.449	>	0.406
Positive Predictive Value	0.625	>	0.560
Total TP	155	>	140
Total TN	36257	>	36255
Total FP	98	<	117
Total FP CONTRA	8	<	14
Total FP INCONS	85	<	96
Total FP COMP	5	<	7
Total FN	190	<	205
P-value	2.10198558684e-08

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

Total Scores
MCC	0.526
Average MCC ± 95% Confidence Intervals	0.503 ± 0.158
Sensitivity	0.449
Positive Predictive Value	0.625
Nr of predictions	13

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...	0.61	0.55	0.69	11	1524	5	0	5	0	9
2LKR_A	-	0.50	0.44	0.59	17	6076	12	2	10	0	22
3AMU_B	tRNA links to Rfam database...	0.67	0.59	0.76	16	2982	7	0	5	2	11
3J0L_2	-	0.39	0.36	0.43	12	6188	18	2	14	2	21
3J0L_a	-	0.22	0.19	0.27	3	1117	8	1	7	0	13
3J0L_7	-	0.30	0.29	0.33	5	1210	10	0	10	0	12
3J0L_g	-	-0.01	0.00	0.00	0	461	4	1	3	0	4
3J16_L	tRNA links to Rfam database...	0.75	0.57	1.00	17	2758	0	0	0	0	13
3SD1_A	THF links to Rfam database...	0.62	0.50	0.78	21	3889	6	0	6	0	21
3U4M_B	-	0.38	0.32	0.46	12	3134	14	0	14	0	25
4AOB_A	SAM links to Rfam database...	0.35	0.26	0.48	11	4348	13	1	11	1	31
4ENB_A	crcB links to Rfam database...	0.89	0.79	1.00	15	1260	0	0	0	0	4
4ENC_A	crcB links to Rfam database...	0.86	0.79	0.94	15	1310	1	1	0	0	4

Total Scores
MCC	0.473
Average MCC ± 95% Confidence Intervals	0.425 ± 0.176
Sensitivity	0.406
Positive Predictive Value	0.560
Nr of predictions	13

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...	-0.01	0.00	0.00	0	1525	15	2	13	0	20
2LKR_A	-	0.52	0.44	0.63	17	6078	12	2	8	2	22
3AMU_B	tRNA links to Rfam database...	0.67	0.59	0.76	16	2982	7	0	5	2	11
3J0L_2	-	0.25	0.24	0.28	8	6187	23	2	19	2	25
3J0L_a	-	0.39	0.31	0.50	5	1118	5	1	4	0	11
3J0L_7	-	-0.01	0.00	0.00	0	1212	13	0	13	0	17
3J0L_g	-	-0.01	0.00	0.00	0	461	4	1	3	0	4
3J16_L	tRNA links to Rfam database...	0.84	0.70	1.00	21	2754	0	0	0	0	9
3SD1_A	THF links to Rfam database...	0.52	0.45	0.61	19	3885	12	2	10	0	23
3U4M_B	-	0.38	0.32	0.46	12	3134	14	0	14	0	25
4AOB_A	SAM links to Rfam database...	0.59	0.48	0.74	20	4344	8	2	5	1	22
4ENB_A	crcB links to Rfam database...	0.70	0.58	0.85	11	1262	2	1	1	0	8
4ENC_A	crcB links to Rfam database...	0.70	0.58	0.85	11	1313	2	1	1	0	8

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