CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	CRWrnafold		MaxExpect
MCC	0.502	>	0.468
Average MCC ± 95% Confidence Intervals	0.510 ± 0.264	>	0.455 ± 0.239
Sensitivity	0.516	>	0.472
Positive Predictive Value	0.503	>	0.481
Total TP	82	>	75
Total TN	10506	<	10513
Total FP	103	>	98
Total FP CONTRA	27	>	26
Total FP INCONS	54	<	55
Total FP COMP	22	>	17
Total FN	77	<	84
P-value	0.0

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

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	0.468
Average MCC ± 95% Confidence Intervals	0.455 ± 0.239
Sensitivity	0.472
Positive Predictive Value	0.481
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	4	1	1	7
3SD1_A	THF links to Rfam database...	0.70	0.69	0.71	20	1505	8	3	5	0	9
3U4M_B	-	0.58	0.59	0.59	13	1254	9	2	7	0	9
4A1C_2	5_8S_rRNA links to Rfam database...	0.19	0.25	0.16	5	4484	41	10	17	14	15
4AOB_A	SAM links to Rfam database...	0.60	0.59	0.63	17	1410	11	4	6	1	12
4ENB_A	crcB links to Rfam database...	0.85	0.73	1.00	11	461	0	0	0	0	4
4ENC_A	crcB links to Rfam database...	0.36	0.33	0.42	5	484	8	0	7	1	10

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