CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	CRWrnafold		Vsfold4
MCC	0.467	>	0.393
Average MCC ± 95% Confidence Intervals	0.424 ± 0.161	>	0.401 ± 0.138
Sensitivity	0.410	>	0.331
Positive Predictive Value	0.540	>	0.475
Total TP	177	>	143
Total TN	55098	<	55125
Total FP	167	<	174
Total FP CONTRA	18	>	13
Total FP INCONS	133	<	145
Total FP COMP	16	=	16
Total FN	255	<	289
P-value	1.59816551561e-08

Comparison of performance of CRWrnafold and Vsfold4. 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 CRWrnafold and Vsfold4).
Comparison of average Matthews Correlation Coefficients (MCCs) for CRWrnafold and Vsfold4. 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 CRWrnafold and Vsfold4).

Total Scores
MCC	0.467
Average MCC ± 95% Confidence Intervals	0.424 ± 0.161
Sensitivity	0.410
Positive Predictive Value	0.540
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...	-0.01	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_g	-	-0.01	0.00	0.00	0	461	4	1	3	0	4
3J0L_a	-	0.39	0.31	0.50	5	1118	5	1	4	0	11
3J0L_2	-	0.25	0.24	0.28	8	6187	23	2	19	2	25
3J0L_7	-	-0.01	0.00	0.00	0	1212	13	0	13	0	17
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
4A1C_2	5_8S_rRNA links to Rfam database...	0.13	0.15	0.13	5	11741	44	4	31	9	28
4A1C_3	5S_rRNA links to Rfam database...	0.70	0.59	0.84	32	7102	6	0	6	0	22
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

Total Scores
MCC	0.393
Average MCC ± 95% Confidence Intervals	0.401 ± 0.138
Sensitivity	0.331
Positive Predictive Value	0.475
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...	-0.01	0.00	0.00	0	1527	13	0	13	0	20
2LKR_A	-	0.31	0.28	0.34	11	6073	21	3	18	0	28
3AMU_B	tRNA links to Rfam database...	0.64	0.56	0.75	15	2983	7	0	5	2	12
3J0L_g	-	-0.01	0.00	0.00	0	461	4	1	3	0	4
3J0L_a	-	0.39	0.31	0.50	5	1118	5	2	3	0	11
3J0L_2	-	0.38	0.36	0.41	12	6187	18	3	14	1	21
3J0L_7	-	0.51	0.41	0.64	7	1214	4	0	4	0	10
3J16_L	tRNA links to Rfam database...	0.82	0.67	1.00	20	2755	0	0	0	0	10
3SD1_A	THF links to Rfam database...	0.19	0.17	0.24	7	3887	22	1	21	0	35
3U4M_B	-	0.38	0.32	0.46	12	3134	14	0	14	0	25
4A1C_2	5_8S_rRNA links to Rfam database...	0.28	0.24	0.33	8	11757	28	0	16	12	25
4A1C_3	5S_rRNA links to Rfam database...	0.26	0.22	0.32	12	7103	25	2	23	0	42
4AOB_A	SAM links to Rfam database...	0.42	0.33	0.54	14	4345	13	1	11	1	28
4ENB_A	crcB links to Rfam database...	0.76	0.58	1.00	11	1264	0	0	0	0	8
4ENC_A	crcB links to Rfam database...	0.69	0.47	1.00	9	1317	0	0	0	0	10

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