CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	ContextFold		Mastr(20)
MCC	0.781	>	0.561
Average MCC ± 95% Confidence Intervals	0.762 ± 0.160	>	0.442 ± 0.244
Sensitivity	0.731	>	0.430
Positive Predictive Value	0.840	>	0.741
Total TP	204	>	120
Total TN	24164	<	24245
Total FP	74	>	54
Total FP CONTRA	13	>	5
Total FP INCONS	26	<	37
Total FP COMP	35	>	12
Total FN	75	<	159
P-value	1.16841705202e-08

Comparison of performance of ContextFold and Mastr(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 Mastr(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 Mastr(20)).
Comparison of average Matthews Correlation Coefficients (MCCs) for ContextFold and Mastr(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 Mastr(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	0.561
Average MCC ± 95% Confidence Intervals	0.442 ± 0.244
Sensitivity	0.430
Positive Predictive Value	0.741
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...	0.26	0.25	0.29	5	1095	12	1	11	0	15
3J2L_3	5S_rRNA links to Rfam database...	0.42	0.38	0.48	13	2993	16	2	12	2	21
3ZEX_C	5_8S_rRNA links to Rfam database...	0.00	0.00	0.00	0	5374	0	0	0	0	29
3ZEX_D	5S_rRNA links to Rfam database...	0.93	0.91	0.94	32	2762	7	0	2	5	3
4A1C_2	5_8S_rRNA links to Rfam database...	0.00	0.00	0.00	0	4516	0	0	0	0	20
4A1C_3	5S_rRNA links to Rfam database...	0.88	0.86	0.89	32	2727	7	0	4	3	5
4AOB_A	SAM links to Rfam database...	0.42	0.34	0.53	10	1418	10	1	8	1	19
4ENB_A	crcB links to Rfam database...	0.44	0.20	1.00	3	469	0	0	0	0	12
4ENC_A	crcB links to Rfam database...	0.57	0.33	1.00	5	491	0	0	0	0	10
4FRG_B	AdoCbl-variant links to Rfam database...	0.00	0.00	0.00	0	1202	0	0	0	0	24

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