CompaRNA - on-line benchmarks of RNA structure prediction methods

FAQ

Metric	Multilign(seed)		PPfold(seed)
MCC	0.526	>	0.152
Average MCC ± 95% Confidence Intervals	0.483 ± 0.276	>	0.095 ± 0.167
Sensitivity	0.402	>	0.038
Positive Predictive Value	0.695	>	0.625
Total TP	107	>	10
Total TN	35984	<	36122
Total FP	49	>	24
Total FP CONTRA	6	>	0
Total FP INCONS	41	>	6
Total FP COMP	2	<	18
Total FN	159	<	256
P-value	0.0

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

Total Scores
MCC	0.526
Average MCC ± 95% Confidence Intervals	0.483 ± 0.276
Sensitivity	0.402
Positive Predictive Value	0.695
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	1	11	0	20
3RKF_A	Purine links to Rfam database...	0.76	0.59	1.00	20	2191	0	0	0	0	14
3SD1_A	THF links to Rfam database...	0.55	0.45	0.68	19	3888	9	1	8	0	23
3W3S_B	tRNA-Sec links to Rfam database...	0.84	0.73	0.97	29	4723	2	0	1	1	11
3ZEX_C	5_8S_rRNA links to Rfam database...	0.39	0.27	0.58	14	14172	10	3	7	0	38
4AOB_A	SAM links to Rfam database...	0.61	0.45	0.83	19	4348	5	0	4	1	23
4FRN_A	AdoCbl-variant links to Rfam database...	0.24	0.17	0.35	6	5134	11	1	10	0	30

Total Scores
MCC	0.152
Average MCC ± 95% Confidence Intervals	0.095 ± 0.167
Sensitivity	0.038
Positive Predictive Value	0.625
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...	0.47	0.30	0.75	6	1532	2	0	2	0	14
3RKF_A	Purine links to Rfam database...	0.00	0.00	0.00	0	2211	0	0	0	0	34
3SD1_A	THF links to Rfam database...	0.00	0.00	0.00	0	3916	0	0	0	0	42
3W3S_B	tRNA-Sec links to Rfam database...	0.00	0.00	0.00	0	4753	0	0	0	0	40
3ZEX_C	5_8S_rRNA links to Rfam database...	0.20	0.08	0.50	4	14188	22	0	4	18	48
4AOB_A	SAM links to Rfam database...	0.00	0.00	0.00	0	4371	0	0	0	0	42
4FRN_A	AdoCbl-variant links to Rfam database...	0.00	0.00	0.00	0	5151	0	0	0	0	36

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