CompaRNA - on-line benchmarks of RNA structure prediction methods

FAQ

Metric	TurboFold(20)		MCFold
MCC	0.630	>	0.498
Average MCC ± 95% Confidence Intervals	0.648 ± 0.179	>	0.519 ± 0.229
Sensitivity	0.516	>	0.512
Positive Predictive Value	0.776	>	0.492
Total TP	128	>	127
Total TN	31477	>	31384
Total FP	48	<	149
Total FP CONTRA	2	<	18
Total FP INCONS	35	<	113
Total FP COMP	11	<	18
Total FN	120	<	121
P-value	0.0

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

Total Scores
MCC	0.630
Average MCC ± 95% Confidence Intervals	0.648 ± 0.179
Sensitivity	0.516
Positive Predictive Value	0.776
Nr of predictions	8

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
3AMU_B	tRNA links to Rfam database...	0.70	0.59	0.84	16	2984	5	0	3	2	11
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
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...	0.18	0.15	0.21	5	11757	28	0	19	9	28
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

Total Scores
MCC	0.498
Average MCC ± 95% Confidence Intervals	0.519 ± 0.229
Sensitivity	0.512
Positive Predictive Value	0.492
Nr of predictions	8

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...	0.97	0.95	1.00	19	971	0	0	0	0	1
3AMU_B	tRNA links to Rfam database...	0.44	0.48	0.42	13	2972	18	2	16	0	14
3RKF_A	Purine links to Rfam database...	0.70	0.65	0.76	22	2182	7	1	6	0	12
3SD1_A	THF links to Rfam database...	0.33	0.33	0.35	14	3876	26	0	26	0	28
4A1C_3	5S_rRNA links to Rfam database...	0.68	0.67	0.71	36	7089	17	1	14	2	18
4A1C_2	5_8S_rRNA links to Rfam database...	0.13	0.15	0.11	5	11735	56	10	31	15	28
4ENB_A	crcB links to Rfam database...	0.61	0.63	0.60	12	1255	8	2	6	0	7
4ENC_A	crcB links to Rfam database...	0.28	0.32	0.27	6	1304	17	2	14	1	13

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