CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	Multilign(20)		Carnac(seed)
MCC	0.560	>	0.269
Average MCC ± 95% Confidence Intervals	0.549 ± 0.253	>	0.100 ± 0.226
Sensitivity	0.524	>	0.073
Positive Predictive Value	0.611	<	1.000
Total TP	129	>	18
Total TN	15476	<	15669
Total FP	94	>	1
Total FP CONTRA	21	>	0
Total FP INCONS	61	>	0
Total FP COMP	12	>	1
Total FN	117	<	228
P-value	5.76570236188e-09

Comparison of performance of Multilign(20) 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 Multilign(20) and Carnac(seed)).
Comparison of performance of Multilign(20) 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 Multilign(20) and Carnac(seed)).
Comparison of average Matthews Correlation Coefficients (MCCs) for Multilign(20) 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 Multilign(20) and Carnac(seed)).
Comparison of average Matthews Correlation Coefficients (MCCs) for Multilign(20) 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 Multilign(20) and Carnac(seed)).

Total Scores
MCC	0.560
Average MCC ± 95% Confidence Intervals	0.549 ± 0.253
Sensitivity	0.524
Positive Predictive Value	0.611
Nr of predictions	10

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2L94_A	HIV_FE links to Rfam database...	1.00	1.00	1.00	18	339	1	0	0	1	0
2XXA_G	Bacteria_small_SRP links to Rfam database...	-0.01	0.00	0.00	0	2033	12	2	10	0	35
3RKF_A	Purine links to Rfam database...	0.91	0.88	0.95	21	844	1	0	1	0	3
3SD1_A	THF links to Rfam database...	0.68	0.69	0.69	20	1504	9	4	5	0	9
4A1C_3	5S_rRNA links to Rfam database...	0.88	0.86	0.89	32	2727	6	0	4	2	5
4A1C_2	5_8S_rRNA links to Rfam database...	0.20	0.25	0.16	5	4485	33	9	17	7	15
4AOB_A	SAM links to Rfam database...	0.59	0.55	0.64	16	1412	10	3	6	1	13
4ENB_A	crcB links to Rfam database...	0.39	0.33	0.50	5	462	6	0	5	1	10
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...	0.13	0.13	0.17	3	1184	15	2	13	0	21

Total Scores
MCC	0.269
Average MCC ± 95% Confidence Intervals	0.100 ± 0.226
Sensitivity	0.073
Positive Predictive Value	1.000
Nr of predictions	10

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2L94_A	HIV_FE links to Rfam database...	1.00	1.00	1.00	18	339	1	0	0	1	0
2XXA_G	Bacteria_small_SRP links to Rfam database...	0.00	0.00	0.00	0	2045	0	0	0	0	35
3RKF_A	Purine links to Rfam database...	0.00	0.00	0.00	0	866	0	0	0	0	24
3SD1_A	THF links to Rfam database...	0.00	0.00	0.00	0	1533	0	0	0	0	29
4A1C_3	5S_rRNA links to Rfam database...	0.00	0.00	0.00	0	2763	0	0	0	0	37
4A1C_2	5_8S_rRNA links to Rfam database...	0.00	0.00	0.00	0	4516	0	0	0	0	20
4AOB_A	SAM links to Rfam database...	0.00	0.00	0.00	0	1437	0	0	0	0	29
4ENB_A	crcB links to Rfam database...	0.00	0.00	0.00	0	472	0	0	0	0	15
4ENC_A	crcB links to Rfam database...	0.00	0.00	0.00	0	496	0	0	0	0	15
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.