CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	PknotsRG		CRWrnafold
MCC	0.586	>	0.502
Average MCC ± 95% Confidence Intervals	0.602 ± 0.260	>	0.510 ± 0.264
Sensitivity	0.616	>	0.516
Positive Predictive Value	0.570	>	0.503
Total TP	98	>	82
Total TN	10497	<	10506
Total FP	88	<	103
Total FP CONTRA	28	>	27
Total FP INCONS	46	<	54
Total FP COMP	14	<	22
Total FN	61	<	77
P-value	0.0

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

Total Scores
MCC	0.586
Average MCC ± 95% Confidence Intervals	0.602 ± 0.260
Sensitivity	0.616
Positive Predictive Value	0.570
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...	0.66	0.61	0.73	11	513	4	2	2	0	7
3J0L_a	-	0.18	0.18	0.22	2	402	8	3	4	1	9
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	4480	43	11	20	12	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...	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

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

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