CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	ContextFold		RNASampler(seed)
MCC	0.394	>	0.333
Average MCC ± 95% Confidence Intervals	0.388 ± 0.238	>	0.326 ± 0.197
Sensitivity	0.322	>	0.224
Positive Predictive Value	0.488	<	0.500
Total TP	79	>	55
Total TN	54707	<	54759
Total FP	122	>	81
Total FP CONTRA	15	>	4
Total FP INCONS	68	>	51
Total FP COMP	39	>	26
Total FN	166	<	190
P-value	0.0

Comparison of performance of ContextFold and RNASampler(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 ContextFold and RNASampler(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 ContextFold and RNASampler(seed)).
Comparison of average Matthews Correlation Coefficients (MCCs) for ContextFold and RNASampler(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 ContextFold and RNASampler(seed)).

Total Scores
MCC	0.394
Average MCC ± 95% Confidence Intervals	0.388 ± 0.238
Sensitivity	0.322
Positive Predictive Value	0.488
Nr of predictions	7

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2LC8_A	GP_knot1 links to Rfam database...	0.55	0.50	0.63	10	1524	6	0	6	0	10
3J3E_8	5_8S_rRNA links to Rfam database...	0.00	0.00	0.00	0	7483	29	9	11	9	33
3J3F_8	5_8S_rRNA links to Rfam database...	0.33	0.31	0.37	11	12216	29	3	16	10	25
3W3S_B	tRNA-Sec links to Rfam database...	0.79	0.70	0.90	28	4722	4	0	3	1	12
3ZEX_C	5_8S_rRNA links to Rfam database...	0.33	0.25	0.45	13	14167	22	1	15	6	39
4A1C_2	5_8S_rRNA links to Rfam database...	0.20	0.15	0.28	5	11763	26	0	13	13	28
4JF2_A	preQ1-II links to Rfam database...	0.50	0.39	0.67	12	2832	6	2	4	0	19

Total Scores
MCC	0.333
Average MCC ± 95% Confidence Intervals	0.326 ± 0.197
Sensitivity	0.224
Positive Predictive Value	0.500
Nr of predictions	7

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2LC8_A	GP_knot1 links to Rfam database...	-0.01	0.00	0.00	0	1530	10	0	10	0	20
3J3E_8	5_8S_rRNA links to Rfam database...	0.12	0.09	0.17	3	7485	22	2	13	7	30
3J3F_8	5_8S_rRNA links to Rfam database...	0.44	0.33	0.57	12	12225	15	1	8	6	24
3W3S_B	tRNA-Sec links to Rfam database...	0.55	0.30	1.00	12	4741	1	0	0	1	28
3ZEX_C	5_8S_rRNA links to Rfam database...	0.32	0.19	0.53	10	14177	13	1	8	4	42
4A1C_2	5_8S_rRNA links to Rfam database...	0.31	0.24	0.40	8	11761	20	0	12	8	25
4JF2_A	preQ1-II links to Rfam database...	0.57	0.32	1.00	10	2840	0	0	0	0	21

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