CompaRNA - on-line benchmarks of RNA structure prediction methods

FAQ

Metric	PETfold_pre2.0(seed)		RNAalifold(20)
MCC	0.803	>	0.620
Average MCC ± 95% Confidence Intervals	0.787 ± 0.086	>	0.620 ± 0.178
Sensitivity	0.752	>	0.573
Positive Predictive Value	0.861	>	0.678
Total TP	155	>	118
Total TN	23007	<	23013
Total FP	68	<	74
Total FP CONTRA	11	<	18
Total FP INCONS	14	<	38
Total FP COMP	43	>	18
Total FN	51	<	88
P-value	1.4651262096e-08

Comparison of performance of PETfold_pre2.0(seed) and RNAalifold(20). 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 RNAalifold(20)).
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 PETfold_pre2.0(seed) and RNAalifold(20)).
Comparison of average Matthews Correlation Coefficients (MCCs) for PETfold_pre2.0(seed) and RNAalifold(20). 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 RNAalifold(20)).

Total Scores
MCC	0.803
Average MCC ± 95% Confidence Intervals	0.787 ± 0.086
Sensitivity	0.752
Positive Predictive Value	0.861
Nr of predictions	10

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
3J20_0	tRNA links to Rfam database...	0.95	0.95	0.95	20	1198	2	1	0	1	1
3J3D_C	tRNA links to Rfam database...	0.90	0.95	0.86	18	947	4	3	0	1	1
3J3E_8	5_8S_rRNA links to Rfam database...	0.71	0.67	0.77	10	2729	8	1	2	5	5
3J3F_8	5_8S_rRNA links to Rfam database...	0.86	0.84	0.89	16	4743	13	2	0	11	3
3ZEX_C	5_8S_rRNA links to Rfam database...	0.70	0.59	0.85	17	5354	12	1	2	9	12
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
4FRG_B	AdoCbl-variant links to Rfam database...	0.87	0.83	0.91	20	1180	3	0	2	1	4

Total Scores
MCC	0.620
Average MCC ± 95% Confidence Intervals	0.620 ± 0.178
Sensitivity	0.573
Positive Predictive Value	0.678
Nr of predictions	10

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
3J20_0	tRNA links to Rfam database...	0.95	0.95	0.95	20	1198	1	1	0	0	1
3J3D_C	tRNA links to Rfam database...	0.87	0.89	0.85	17	948	3	3	0	0	2
3J3E_8	5_8S_rRNA links to Rfam database...	0.34	0.33	0.36	5	2728	9	3	6	0	10
3J3F_8	5_8S_rRNA links to Rfam database...	0.54	0.58	0.50	11	4739	20	4	7	9	8
3ZEX_C	5_8S_rRNA links to Rfam database...	0.46	0.41	0.52	12	5351	16	2	9	5	17
4A1C_2	5_8S_rRNA links to Rfam database...	0.22	0.25	0.19	5	4490	23	5	16	2	15
4AOB_A	SAM links to Rfam database...	0.85	0.72	1.00	21	1416	2	0	0	2	8
4ENB_A	crcB links to Rfam database...	0.51	0.27	1.00	4	468	0	0	0	0	11
4ENC_A	crcB links to Rfam database...	0.63	0.40	1.00	6	490	0	0	0	0	9
4FRG_B	AdoCbl-variant links to Rfam database...	0.84	0.71	1.00	17	1185	0	0	0	0	7

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