CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	ContextFold		MXScarna(20)
MCC	0.660	>	0.564
Average MCC ± 95% Confidence Intervals	0.661 ± 0.151	>	0.558 ± 0.155
Sensitivity	0.525	>	0.456
Positive Predictive Value	0.835	>	0.703
Total TP	213	>	185
Total TN	63992	>	63984
Total FP	65	<	99
Total FP CONTRA	4	<	11
Total FP INCONS	38	<	67
Total FP COMP	23	>	21
Total FN	193	<	221
P-value	1.58287649515e-08

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	0.660
Average MCC ± 95% Confidence Intervals	0.661 ± 0.151
Sensitivity	0.525
Positive Predictive Value	0.835
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...	0.84	0.70	1.00	21	2829	1	0	0	1	9
3J20_1	tRNA links to Rfam database...	0.96	0.91	1.00	21	2905	0	0	0	0	2
3J2L_3	5S_rRNA links to Rfam database...	0.79	0.62	1.00	33	7842	2	0	0	2	20
3ZEX_C	5_8S_rRNA links to Rfam database...	0.33	0.25	0.45	13	14167	22	1	15	6	39
3ZEX_D	5S_rRNA links to Rfam database...	0.81	0.67	0.97	33	6987	1	0	1	0	16
4A1C_2	5_8S_rRNA links to Rfam database...	0.20	0.15	0.28	5	11763	26	0	13	13	28
4A1C_3	5S_rRNA links to Rfam database...	0.78	0.63	0.97	34	7105	1	0	1	0	20
4AOB_A	SAM links to Rfam database...	0.52	0.40	0.68	17	4346	9	1	7	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
4FRG_B	AdoCbl-variant links to Rfam database...	0.71	0.56	0.90	18	3466	2	1	1	0	14

Total Scores
MCC	0.564
Average MCC ± 95% Confidence Intervals	0.558 ± 0.155
Sensitivity	0.456
Positive Predictive Value	0.703
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...	0.82	0.67	1.00	20	2830	0	0	0	0	10
3J20_1	tRNA links to Rfam database...	0.93	0.87	1.00	20	2906	0	0	0	0	3
3J2L_3	5S_rRNA links to Rfam database...	0.54	0.42	0.71	22	7844	11	1	8	2	31
3ZEX_C	5_8S_rRNA links to Rfam database...	0.31	0.21	0.46	11	14172	13	2	11	0	41
3ZEX_D	5S_rRNA links to Rfam database...	0.68	0.63	0.74	31	6979	11	2	9	0	18
4A1C_2	5_8S_rRNA links to Rfam database...	0.18	0.15	0.21	5	11757	36	2	17	17	28
4A1C_3	5S_rRNA links to Rfam database...	0.64	0.56	0.75	30	7100	11	2	8	1	24
4AOB_A	SAM links to Rfam database...	0.62	0.55	0.72	23	4339	10	0	9	1	19
4ENB_A	crcB links to Rfam database...	0.26	0.11	0.67	2	1272	1	0	1	0	17
4ENC_A	crcB links to Rfam database...	0.60	0.37	1.00	7	1319	0	0	0	0	12
4FRG_B	AdoCbl-variant links to Rfam database...	0.55	0.44	0.70	14	3466	6	2	4	0	18

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