CompaRNA - on-line benchmarks of RNA structure prediction methods

FAQ

Metric	CentroidAlifold(20)		TurboFold(seed)
MCC	0.569	>	0.510
Average MCC ± 95% Confidence Intervals	0.533 ± 0.165	<	0.542 ± 0.163
Sensitivity	0.391	<	0.419
Positive Predictive Value	0.833	>	0.626
Total TP	150	<	161
Total TN	66775	>	66698
Total FP	34	<	132
Total FP CONTRA	3	<	12
Total FP INCONS	27	<	84
Total FP COMP	4	<	36
Total FN	234	>	223
P-value	1.39551335374e-08

Comparison of performance of CentroidAlifold(20) and TurboFold(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 CentroidAlifold(20) and TurboFold(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 CentroidAlifold(20) and TurboFold(seed)).
Comparison of average Matthews Correlation Coefficients (MCCs) for CentroidAlifold(20) and TurboFold(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 CentroidAlifold(20) and TurboFold(seed)).

Total Scores
MCC	0.569
Average MCC ± 95% Confidence Intervals	0.533 ± 0.165
Sensitivity	0.391
Positive Predictive Value	0.833
Nr of predictions	11

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2L94_A	HIV_FE links to Rfam database...	0.61	0.55	0.69	11	974	5	0	5	0	9
3J3E_8	5_8S_rRNA links to Rfam database...	0.00	0.00	0.00	0	7499	4	0	4	0	33
3J3F_8	5_8S_rRNA links to Rfam database...	0.39	0.25	0.60	9	12231	6	1	5	0	27
3RKF_A	Purine links to Rfam database...	0.72	0.53	1.00	18	2193	0	0	0	0	16
3SD1_A	THF links to Rfam database...	0.71	0.52	0.96	22	3893	1	0	1	0	20
3ZEX_C	5_8S_rRNA links to Rfam database...	0.38	0.21	0.69	11	14180	5	1	4	0	41
4A1C_3	5S_rRNA links to Rfam database...	0.76	0.63	0.92	34	7103	4	0	3	1	20
4A1C_2	5_8S_rRNA links to Rfam database...	0.26	0.15	0.45	5	11770	8	1	5	2	28
4AOB_A	SAM links to Rfam database...	0.75	0.57	1.00	24	4347	1	0	0	1	18
4ENB_A	crcB links to Rfam database...	0.69	0.47	1.00	9	1266	0	0	0	0	10
4ENC_A	crcB links to Rfam database...	0.60	0.37	1.00	7	1319	0	0	0	0	12

Total Scores
MCC	0.510
Average MCC ± 95% Confidence Intervals	0.542 ± 0.163
Sensitivity	0.419
Positive Predictive Value	0.626
Nr of predictions	11

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2L94_A	HIV_FE links to Rfam database...	0.92	0.90	0.95	18	971	1	0	1	0	2
3J3E_8	5_8S_rRNA links to Rfam database...	0.17	0.15	0.21	5	7479	28	2	17	9	28
3J3F_8	5_8S_rRNA links to Rfam database...	0.39	0.36	0.42	13	12215	32	2	16	14	23
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...	0.59	0.48	0.74	20	3889	7	1	6	0	22
3ZEX_C	5_8S_rRNA links to Rfam database...	0.39	0.27	0.56	14	14171	14	2	9	3	38
4A1C_3	5S_rRNA links to Rfam database...	0.69	0.57	0.84	31	7103	6	0	6	0	23
4A1C_2	5_8S_rRNA links to Rfam database...	0.15	0.15	0.15	5	11748	37	3	25	9	28
4AOB_A	SAM links to Rfam database...	0.56	0.40	0.77	17	4349	6	1	4	1	25
4ENB_A	crcB links to Rfam database...	0.69	0.47	1.00	9	1266	0	0	0	0	10
4ENC_A	crcB links to Rfam database...	0.65	0.47	0.90	9	1316	1	1	0	0	10

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