CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	ContextFold		RNAalifold(seed)
MCC	0.665	>	0.652
Average MCC ± 95% Confidence Intervals	0.558 ± 0.138	>	0.541 ± 0.164
Sensitivity	0.549	>	0.506
Positive Predictive Value	0.808	<	0.839
Total TP	508	>	469
Total TN	1164015	<	1164085
Total FP	145	>	98
Total FP CONTRA	15	>	6
Total FP INCONS	106	>	84
Total FP COMP	24	>	8
Total FN	418	<	457
P-value	2.28582059552e-06

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

Total Scores
MCC	0.665
Average MCC ± 95% Confidence Intervals	0.558 ± 0.138
Sensitivity	0.549
Positive Predictive Value	0.808
Nr of predictions	10

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
3J20_2	SSU_rRNA_archaea links to Rfam database...	0.73	0.61	0.87	387	1116318	63	8	52	3	246
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
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
4FRN_A	AdoCbl-variant links to Rfam database...	0.40	0.33	0.50	12	5127	12	3	9	0	24

Total Scores
MCC	0.652
Average MCC ± 95% Confidence Intervals	0.541 ± 0.164
Sensitivity	0.506
Positive Predictive Value	0.839
Nr of predictions	10

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	1528	12	0	12	0	20
3J20_2	SSU_rRNA_archaea links to Rfam database...	0.69	0.58	0.83	367	1116322	80	5	71	4	266
3W3S_B	tRNA-Sec links to Rfam database...	0.67	0.45	1.00	18	4735	1	0	0	1	22
3ZEX_C	5_8S_rRNA links to Rfam database...	0.42	0.17	1.00	9	14187	0	0	0	0	43
4A1C_2	5_8S_rRNA links to Rfam database...	0.39	0.15	1.00	5	11776	2	0	0	2	28
4AOB_A	SAM links to Rfam database...	0.72	0.52	1.00	22	4349	1	0	0	1	20
4ENB_A	crcB links to Rfam database...	0.56	0.32	1.00	6	1269	0	0	0	0	13
4ENC_A	crcB links to Rfam database...	0.56	0.32	1.00	6	1320	0	0	0	0	13
4FRG_B	AdoCbl-variant links to Rfam database...	0.73	0.53	1.00	17	3469	0	0	0	0	15
4FRN_A	AdoCbl-variant links to Rfam database...	0.69	0.53	0.90	19	5130	2	1	1	0	17

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