CompaRNA - on-line benchmarks of RNA structure prediction methods

FAQ

Metric	Afold		RNAalifold(seed)
MCC	0.567	>	0.558
Average MCC ± 95% Confidence Intervals	0.663 ± 0.189	>	0.570 ± 0.163
Sensitivity	0.617	>	0.406
Positive Predictive Value	0.526	<	0.772
Total TP	222	>	146
Total TN	64335	<	64568
Total FP	256	>	55
Total FP CONTRA	91	>	23
Total FP INCONS	109	>	20
Total FP COMP	56	>	12
Total FN	138	<	214
P-value	0.000382312754694

Comparison of performance of Afold and RNAalifold(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 Afold and RNAalifold(seed)).
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 Afold and RNAalifold(seed)).
Comparison of average Matthews Correlation Coefficients (MCCs) for Afold and RNAalifold(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 Afold and RNAalifold(seed)).

Total Scores
MCC	0.567
Average MCC ± 95% Confidence Intervals	0.663 ± 0.189
Sensitivity	0.617
Positive Predictive Value	0.526
Nr of predictions	11

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...	0.64	0.61	0.69	11	512	6	0	5	1	7
3A3A_A	tRNA-Sec links to Rfam database...	0.93	0.87	1.00	26	1474	0	0	0	0	4
3IVN_B	Purine links to Rfam database...	0.91	0.83	1.00	19	884	0	0	0	0	4
3IYQ_A	tmRNA links to Rfam database...	0.23	0.33	0.17	17	22339	97	47	37	13	34
3IZ4_A	tmRNA links to Rfam database...	0.52	0.57	0.48	54	25423	63	27	32	4	41
3LA5_A	Purine links to Rfam database...	0.91	0.84	1.00	21	933	0	0	0	0	4
3NPB_A	SAM links to Rfam database...	0.82	0.73	0.93	27	2249	6	0	2	4	10
3O58_3	5_8S_rRNA links to Rfam database...	0.41	0.50	0.34	11	4732	38	6	15	17	11
3RKF_A	Purine links to Rfam database...	0.91	0.83	1.00	20	846	0	0	0	0	4
4A1C_2	5_8S_rRNA links to Rfam database...	0.19	0.25	0.15	5	4483	43	11	17	15	15
4ENB_A	crcB links to Rfam database...	0.81	0.73	0.92	11	460	3	0	1	2	4

Total Scores
MCC	0.558
Average MCC ± 95% Confidence Intervals	0.570 ± 0.163
Sensitivity	0.406
Positive Predictive Value	0.772
Nr of predictions	11

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	516	12	0	12	0	18
3A3A_A	tRNA-Sec links to Rfam database...	0.79	0.63	1.00	19	1481	0	0	0	0	11
3IVN_B	Purine links to Rfam database...	0.71	0.65	0.79	15	884	4	2	2	0	8
3IYQ_A	tmRNA links to Rfam database...	0.36	0.27	0.48	14	22411	19	13	2	4	37
3IZ4_A	tmRNA links to Rfam database...	0.46	0.26	0.81	25	25505	8	6	0	2	70
3LA5_A	Purine links to Rfam database...	0.73	0.64	0.84	16	935	3	1	2	0	9
3NPB_A	SAM links to Rfam database...	0.77	0.59	1.00	22	2256	3	0	0	3	15
3O58_3	5_8S_rRNA links to Rfam database...	0.60	0.36	1.00	8	4756	1	0	0	1	14
3RKF_A	Purine links to Rfam database...	0.74	0.67	0.84	16	847	3	1	2	0	8
4A1C_2	5_8S_rRNA links to Rfam database...	0.50	0.25	1.00	5	4511	2	0	0	2	15
4ENB_A	crcB links to Rfam database...	0.63	0.40	1.00	6	466	0	0	0	0	9

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