CompaRNA - on-line benchmarks of RNA structure prediction methods

FAQ

Metric	PETfold_pre2.0(seed)		Pknots
MCC	0.828	>	0.531
Average MCC ± 95% Confidence Intervals	0.777 ± 0.178	>	0.626 ± 0.296
Sensitivity	0.772	>	0.556
Positive Predictive Value	0.892	>	0.519
Total TP	132	>	95
Total TN	12516	>	12481
Total FP	42	<	115
Total FP CONTRA	3	<	20
Total FP INCONS	13	<	68
Total FP COMP	26	<	27
Total FN	39	<	76
P-value	0.0

Comparison of performance of PETfold_pre2.0(seed) and Pknots. 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 PETfold_pre2.0(seed) and Pknots).
Comparison of average Matthews Correlation Coefficients (MCCs) for PETfold_pre2.0(seed) and Pknots. 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 PETfold_pre2.0(seed) and Pknots).

Total Scores
MCC	0.828
Average MCC ± 95% Confidence Intervals	0.777 ± 0.178
Sensitivity	0.772
Positive Predictive Value	0.892
Nr of predictions	8

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...	0.41	0.33	0.55	6	517	5	0	5	0	12
3J16_L	tRNA links to Rfam database...	1.00	1.00	1.00	21	1138	1	0	0	1	0
3UZL_B	tRNA links to Rfam database...	0.93	0.88	1.00	14	1279	8	0	0	8	2
4A1C_3	5S_rRNA links to Rfam database...	1.00	1.00	1.00	37	2726	2	0	0	2	0
4A1C_2	5_8S_rRNA links to Rfam database...	0.79	0.75	0.83	15	4498	12	1	2	9	5
4AOB_A	SAM links to Rfam database...	0.85	0.79	0.92	23	1412	4	0	2	2	6
4ENB_A	crcB links to Rfam database...	0.61	0.53	0.73	8	461	5	1	2	2	7
4ENC_A	crcB links to Rfam database...	0.61	0.53	0.73	8	485	5	1	2	2	7

Total Scores
MCC	0.531
Average MCC ± 95% Confidence Intervals	0.626 ± 0.296
Sensitivity	0.556
Positive Predictive Value	0.519
Nr of predictions	8

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...	0.83	0.83	0.83	15	510	3	2	1	0	3
3J16_L	tRNA links to Rfam database...	0.41	0.43	0.41	9	1137	13	1	12	0	12
3UZL_B	tRNA links to Rfam database...	1.00	1.00	1.00	16	1277	7	0	0	7	0
4A1C_3	5S_rRNA links to Rfam database...	0.28	0.30	0.28	11	2723	30	4	25	1	26
4A1C_2	5_8S_rRNA links to Rfam database...	0.33	0.40	0.29	8	4488	36	9	11	16	12
4AOB_A	SAM links to Rfam database...	0.19	0.21	0.21	6	1409	23	3	19	1	23
4ENB_A	crcB links to Rfam database...	1.00	1.00	1.00	15	457	2	0	0	2	0
4ENC_A	crcB links to Rfam database...	0.97	1.00	0.94	15	480	1	1	0	0	0

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