CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	ContextFold		Carnac(seed)
MCC	0.672	>	0.479
Average MCC ± 95% Confidence Intervals	0.578 ± 0.131	>	0.094 ± 0.142
Sensitivity	0.553	>	0.260
Positive Predictive Value	0.816	<	0.882
Total TP	542	>	255
Total TN	1171120	<	1171495
Total FP	146	>	36
Total FP CONTRA	15	>	3
Total FP INCONS	107	>	31
Total FP COMP	24	>	2
Total FN	438	<	725
P-value	1.86109605532e-08

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

Total Scores
MCC	0.672
Average MCC ± 95% Confidence Intervals	0.578 ± 0.131
Sensitivity	0.553
Positive Predictive Value	0.816
Nr of predictions	11

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_3	5S_rRNA links to Rfam database...	0.78	0.63	0.97	34	7105	1	0	1	0	20
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	0.479
Average MCC ± 95% Confidence Intervals	0.094 ± 0.142
Sensitivity	0.260
Positive Predictive Value	0.882
Nr of predictions	11

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...	0.44	0.20	1.00	4	1536	0	0	0	0	16
3J20_2	SSU_rRNA_archaea links to Rfam database...	0.59	0.40	0.88	251	1116480	36	3	31	2	382
3W3S_B	tRNA-Sec links to Rfam database...	0.00	0.00	0.00	0	4753	0	0	0	0	40
3ZEX_C	5_8S_rRNA links to Rfam database...	0.00	0.00	0.00	0	14196	0	0	0	0	52
4A1C_3	5S_rRNA links to Rfam database...	0.00	0.00	0.00	0	7140	0	0	0	0	54
4A1C_2	5_8S_rRNA links to Rfam database...	0.00	0.00	0.00	0	11781	0	0	0	0	33
4AOB_A	SAM links to Rfam database...	0.00	0.00	0.00	0	4371	0	0	0	0	42
4ENB_A	crcB links to Rfam database...	0.00	0.00	0.00	0	1275	0	0	0	0	19
4ENC_A	crcB links to Rfam database...	0.00	0.00	0.00	0	1326	0	0	0	0	19
4FRG_B	AdoCbl-variant links to Rfam database...	0.00	0.00	0.00	0	3486	0	0	0	0	32
4FRN_A	AdoCbl-variant links to Rfam database...	0.00	0.00	0.00	0	5151	0	0	0	0	36

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