CompaRNA - on-line benchmarks of RNA structure prediction methods

FAQ

Metric	Murlet(seed)		RNAwolf
MCC	0.451	>	0.370
Average MCC ± 95% Confidence Intervals	0.448 ± 0.192	>	0.384 ± 0.190
Sensitivity	0.268	<	0.344
Positive Predictive Value	0.767	>	0.407
Total TP	56	<	72
Total TN	26347	>	26243
Total FP	18	<	115
Total FP CONTRA	1	<	13
Total FP INCONS	16	<	92
Total FP COMP	1	<	10
Total FN	153	>	137
P-value	0.0

Comparison of performance of Murlet(seed) and RNAwolf. 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 Murlet(seed) and RNAwolf).
Comparison of average Matthews Correlation Coefficients (MCCs) for Murlet(seed) and RNAwolf. 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 Murlet(seed) and RNAwolf).

Total Scores
MCC	0.451
Average MCC ± 95% Confidence Intervals	0.448 ± 0.192
Sensitivity	0.268
Positive Predictive Value	0.767
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...	-0.01	0.00	0.00	0	1528	12	0	12	0	20
3RKF_A	Purine links to Rfam database...	0.53	0.35	0.80	12	2196	3	1	2	0	22
3SD1_A	THF links to Rfam database...	0.47	0.26	0.85	11	3903	2	0	2	0	31
4A1C_2	5_8S_rRNA links to Rfam database...	0.46	0.21	1.00	7	11774	0	0	0	0	26
4AOB_A	SAM links to Rfam database...	0.58	0.33	1.00	14	4357	1	0	0	1	28
4ENB_A	crcB links to Rfam database...	0.56	0.32	1.00	6	1269	0	0	0	0	13
4ENC_A	crcB links to Rfam database...	0.56	0.32	1.00	6	1320	0	0	0	0	13

Total Scores
MCC	0.370
Average MCC ± 95% Confidence Intervals	0.384 ± 0.190
Sensitivity	0.344
Positive Predictive Value	0.407
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...	0.52	0.50	0.56	10	1522	8	0	8	0	10
3RKF_A	Purine links to Rfam database...	0.72	0.62	0.84	21	2186	4	0	4	0	13
3SD1_A	THF links to Rfam database...	0.46	0.43	0.50	18	3880	18	0	18	0	24
4A1C_2	5_8S_rRNA links to Rfam database...	0.08	0.09	0.08	3	11741	46	10	27	9	30
4AOB_A	SAM links to Rfam database...	0.23	0.19	0.30	8	4344	20	1	18	1	34
4ENB_A	crcB links to Rfam database...	0.35	0.32	0.40	6	1260	9	1	8	0	13
4ENC_A	crcB links to Rfam database...	0.34	0.32	0.38	6	1310	10	1	9	0	13

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