CompaRNA - on-line benchmarks of RNA structure prediction methods

FAQ

Metric	RNAshapes		PPfold(seed)
MCC	0.611	>	0.155
Average MCC ± 95% Confidence Intervals	0.619 ± 0.240	>	0.084 ± 0.169
Sensitivity	0.607	>	0.047
Positive Predictive Value	0.628	>	0.538
Total TP	91	>	7
Total TN	9703	<	9835
Total FP	72	>	25
Total FP CONTRA	19	>	0
Total FP INCONS	35	>	6
Total FP COMP	18	<	19
Total FN	59	<	143
P-value	0.0

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

Total Scores
MCC	0.611
Average MCC ± 95% Confidence Intervals	0.619 ± 0.240
Sensitivity	0.607
Positive Predictive Value	0.628
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
3RKF_A	Purine links to Rfam database...	0.91	0.83	1.00	20	846	0	0	0	0	4
3SD1_A	THF links to Rfam database...	0.77	0.76	0.79	22	1505	6	4	2	0	7
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

Total Scores
MCC	0.155
Average MCC ± 95% Confidence Intervals	0.084 ± 0.169
Sensitivity	0.047
Positive Predictive Value	0.538
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...	0.49	0.33	0.75	6	520	2	0	2	0	12
3RKF_A	Purine links to Rfam database...	0.00	0.00	0.00	0	866	0	0	0	0	24
3SD1_A	THF links to Rfam database...	0.00	0.00	0.00	0	1533	0	0	0	0	29
4A1C_2	5_8S_rRNA links to Rfam database...	0.10	0.05	0.20	1	4511	23	0	4	19	19
4AOB_A	SAM links to Rfam database...	0.00	0.00	0.00	0	1437	0	0	0	0	29
4ENB_A	crcB links to Rfam database...	0.00	0.00	0.00	0	472	0	0	0	0	15
4ENC_A	crcB links to Rfam database...	0.00	0.00	0.00	0	496	0	0	0	0	15

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