CompaRNA - on-line benchmarks of RNA structure prediction methods

FAQ

Metric	RNASampler(seed)		RNAwolf
MCC	0.497	>	0.424
Average MCC ± 95% Confidence Intervals	0.476 ± 0.217	>	0.431 ± 0.248
Sensitivity	0.412	<	0.464
Positive Predictive Value	0.608	>	0.397
Total TP	87	<	98
Total TN	23248	>	23144
Total FP	86	<	191
Total FP CONTRA	16	<	51
Total FP INCONS	40	<	98
Total FP COMP	30	<	42
Total FN	124	>	113
P-value	0.0

Comparison of performance of RNASampler(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 RNASampler(seed) and RNAwolf).
Average Matthews Correlation Coefficients (MCC) with 95% confidence intervals (CIs) were plotted for different RNA families, for which at least 3 members were present in the benchmarking dataset. 'n' denotes the number of MCCs used to calculate the average and CI. See tables below for raw data (individual counts for RNASampler(seed) and RNAwolf).
Comparison of average Matthews Correlation Coefficients (MCCs) for RNASampler(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 RNASampler(seed) and RNAwolf).

Total Scores
MCC	0.497
Average MCC ± 95% Confidence Intervals	0.476 ± 0.217
Sensitivity	0.412
Positive Predictive Value	0.608
Nr of predictions	9

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	518	10	0	10	0	18
3J3E_8	5_8S_rRNA links to Rfam database...	0.18	0.20	0.18	3	2725	22	5	9	8	12
3J3F_8	5_8S_rRNA links to Rfam database...	0.47	0.47	0.47	9	4742	18	5	5	8	10
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...	0.72	0.55	0.94	16	1516	1	0	1	0	13
3W3S_B	tRNA-Sec links to Rfam database...	0.60	0.36	1.00	12	1977	1	0	0	1	21
3ZEX_C	5_8S_rRNA links to Rfam database...	0.39	0.31	0.50	9	5356	14	2	7	5	20
4A1C_2	5_8S_rRNA links to Rfam database...	0.40	0.40	0.40	8	4496	20	4	8	8	12
4JF2_A	preQ1-II links to Rfam database...	0.64	0.42	1.00	10	1072	0	0	0	0	14

Total Scores
MCC	0.424
Average MCC ± 95% Confidence Intervals	0.431 ± 0.248
Sensitivity	0.464
Positive Predictive Value	0.397
Nr of predictions	9

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	9	512	7	0	7	0	9
3J3E_8	5_8S_rRNA links to Rfam database...	-0.01	0.00	0.00	0	2719	37	6	17	14	15
3J3F_8	5_8S_rRNA links to Rfam database...	0.28	0.37	0.23	7	4730	39	9	15	15	12
3RKF_A	Purine links to Rfam database...	0.89	0.83	0.95	20	845	1	0	1	0	4
3SD1_A	THF links to Rfam database...	0.58	0.59	0.59	17	1504	12	2	10	0	12
3W3S_B	tRNA-Sec links to Rfam database...	0.70	0.70	0.72	23	1957	10	0	9	1	10
3ZEX_C	5_8S_rRNA links to Rfam database...	0.08	0.10	0.07	3	5328	43	18	25	0	26
4A1C_2	5_8S_rRNA links to Rfam database...	0.12	0.15	0.10	3	4487	38	12	14	12	17
4JF2_A	preQ1-II links to Rfam database...	0.72	0.67	0.80	16	1062	4	4	0	0	8

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