CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	CRWrnafold		RNAsubopt
MCC	0.502	>	0.460
Average MCC ± 95% Confidence Intervals	0.510 ± 0.264	>	0.445 ± 0.244
Sensitivity	0.516	>	0.478
Positive Predictive Value	0.503	>	0.458
Total TP	82	>	76
Total TN	10506	>	10503
Total FP	103	<	107
Total FP CONTRA	27	<	30
Total FP INCONS	54	<	60
Total FP COMP	22	>	17
Total FN	77	<	83
P-value	0.0

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

Total Scores
MCC	0.502
Average MCC ± 95% Confidence Intervals	0.510 ± 0.264
Sensitivity	0.516
Positive Predictive Value	0.503
Nr of predictions	8

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...	-0.03	0.00	0.00	0	513	15	3	12	0	18
3J0L_a	-	0.39	0.36	0.44	4	402	6	3	2	1	7
3SD1_A	THF links to Rfam database...	0.63	0.66	0.61	19	1502	12	6	6	0	10
3U4M_B	-	0.49	0.55	0.46	12	1250	14	3	11	0	10
4A1C_2	5_8S_rRNA links to Rfam database...	0.19	0.25	0.15	5	4483	44	8	20	16	15
4AOB_A	SAM links to Rfam database...	0.71	0.69	0.74	20	1410	8	4	3	1	9
4ENB_A	crcB links to Rfam database...	0.85	0.73	1.00	11	461	2	0	0	2	4
4ENC_A	crcB links to Rfam database...	0.85	0.73	1.00	11	485	2	0	0	2	4

Total Scores
MCC	0.460
Average MCC ± 95% Confidence Intervals	0.445 ± 0.244
Sensitivity	0.478
Positive Predictive Value	0.458
Nr of predictions	8

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...	-0.03	0.00	0.00	0	513	15	3	12	0	18
3J0L_a	-	0.35	0.36	0.36	4	400	8	3	4	1	7
3SD1_A	THF links to Rfam database...	0.73	0.72	0.75	21	1505	7	4	3	0	8
3U4M_B	-	0.49	0.55	0.46	12	1250	14	3	11	0	10
4A1C_2	5_8S_rRNA links to Rfam database...	0.18	0.25	0.14	5	4481	43	13	17	13	15
4AOB_A	SAM links to Rfam database...	0.62	0.62	0.64	18	1409	11	4	6	1	11
4ENB_A	crcB links to Rfam database...	0.85	0.73	1.00	11	461	2	0	0	2	4
4ENC_A	crcB links to Rfam database...	0.36	0.33	0.42	5	484	7	0	7	0	10

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