CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	ContextFold		MXScarna(20)
MCC	0.781	>	0.670
Average MCC ± 95% Confidence Intervals	0.762 ± 0.160	>	0.646 ± 0.171
Sensitivity	0.731	>	0.627
Positive Predictive Value	0.840	>	0.723
Total TP	204	>	175
Total TN	24164	<	24165
Total FP	74	<	109
Total FP CONTRA	13	<	19
Total FP INCONS	26	<	48
Total FP COMP	35	<	42
Total FN	75	<	104
P-value	9.07229227445e-09

Comparison of performance of ContextFold and MXScarna(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 ContextFold and MXScarna(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 ContextFold and MXScarna(20)).
Comparison of average Matthews Correlation Coefficients (MCCs) for ContextFold and MXScarna(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 ContextFold and MXScarna(20)).

Total Scores
MCC	0.781
Average MCC ± 95% Confidence Intervals	0.762 ± 0.160
Sensitivity	0.731
Positive Predictive Value	0.840
Nr of predictions	11

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
3J20_1	tRNA links to Rfam database...	1.00	1.00	1.00	20	1092	1	0	0	1	0
3J2L_3	5S_rRNA links to Rfam database...	0.95	0.91	1.00	31	2989	4	0	0	4	3
3ZEX_C	5_8S_rRNA links to Rfam database...	0.44	0.41	0.48	12	5349	23	4	9	10	17
3ZEX_D	5S_rRNA links to Rfam database...	0.92	0.86	1.00	30	2766	4	0	0	4	5
4A1C_2	5_8S_rRNA links to Rfam database...	0.26	0.25	0.28	5	4498	26	3	10	13	15
4A1C_3	5S_rRNA links to Rfam database...	0.96	0.92	1.00	34	2729	1	0	0	1	3
4AOB_A	SAM links to Rfam database...	0.62	0.59	0.68	17	1412	9	2	6	1	12
4ENB_A	crcB links to Rfam database...	0.77	0.60	1.00	9	463	0	0	0	0	6
4ENC_A	crcB links to Rfam database...	0.73	0.60	0.90	9	486	1	1	0	0	6
4FRG_B	AdoCbl-variant links to Rfam database...	0.77	0.71	0.85	17	1182	3	2	1	0	7

Total Scores
MCC	0.670
Average MCC ± 95% Confidence Intervals	0.646 ± 0.171
Sensitivity	0.627
Positive Predictive Value	0.723
Nr of predictions	11

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
3J20_0	tRNA links to Rfam database...	0.93	0.90	0.95	19	1199	1	1	0	0	2
3J20_1	tRNA links to Rfam database...	0.97	0.95	1.00	19	1093	1	0	0	1	1
3J2L_3	5S_rRNA links to Rfam database...	0.67	0.65	0.71	22	2989	11	3	6	2	12
3ZEX_C	5_8S_rRNA links to Rfam database...	0.35	0.31	0.41	9	5352	15	3	10	2	20
3ZEX_D	5S_rRNA links to Rfam database...	0.85	0.83	0.88	29	2763	13	0	4	9	6
4A1C_2	5_8S_rRNA links to Rfam database...	0.22	0.25	0.21	5	4492	36	8	11	17	15
4A1C_3	5S_rRNA links to Rfam database...	0.80	0.78	0.83	29	2728	12	0	6	6	8
4AOB_A	SAM links to Rfam database...	0.68	0.69	0.69	20	1408	13	2	7	4	9
4ENB_A	crcB links to Rfam database...	0.29	0.13	0.67	2	469	1	0	1	0	13
4ENC_A	crcB links to Rfam database...	0.68	0.47	1.00	7	489	0	0	0	0	8
4FRG_B	AdoCbl-variant links to Rfam database...	0.65	0.58	0.74	14	1183	6	2	3	1	10

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