CompaRNA - on-line benchmarks of RNA structure prediction methods

FAQ

Metric	ContextFold		RNAshapes
MCC	0.662	>	0.473
Average MCC ± 95% Confidence Intervals	0.676 ± 0.208	>	0.476 ± 0.227
Sensitivity	0.608	>	0.485
Positive Predictive Value	0.731	>	0.477
Total TP	79	>	63
Total TN	9028	>	9004
Total FP	44	<	88
Total FP CONTRA	6	<	21
Total FP INCONS	23	<	48
Total FP COMP	15	<	19
Total FN	51	<	67
P-value	0.0

Comparison of performance of ContextFold and RNAshapes. 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 ContextFold and RNAshapes).
Comparison of average Matthews Correlation Coefficients (MCCs) for ContextFold and RNAshapes. 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 ContextFold and RNAshapes).

Total Scores
MCC	0.662
Average MCC ± 95% Confidence Intervals	0.676 ± 0.208
Sensitivity	0.608
Positive Predictive Value	0.731
Nr of predictions	7

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...	0.58	0.56	0.63	10	512	6	0	6	0	8
3J0L_a	-	0.80	0.73	0.89	8	402	2	0	1	1	3
3U4M_B	-	0.98	0.95	1.00	21	1255	0	0	0	0	1
4A1C_2	5_8S_rRNA links to Rfam database...	0.26	0.25	0.28	5	4498	26	3	10	13	15
4AOB_A	SAM links to Rfam database...	0.62	0.59	0.68	17	1412	9	2	6	1	12
4ENB_A	crcB links to Rfam database...	0.77	0.60	1.00	9	463	0	0	0	0	6
4ENC_A	crcB links to Rfam database...	0.73	0.60	0.90	9	486	1	1	0	0	6

Total Scores
MCC	0.473
Average MCC ± 95% Confidence Intervals	0.476 ± 0.227
Sensitivity	0.485
Positive Predictive Value	0.477
Nr of predictions	7

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...	0.64	0.61	0.69	11	512	5	0	5	0	7
3J0L_a	-	0.18	0.18	0.22	2	402	8	3	4	1	9
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	0.16	5	4484	41	11	16	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	2	0	0	2	4
4ENC_A	crcB links to Rfam database...	0.37	0.33	0.45	5	485	7	0	6	1	10

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