CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	RDfolder		Carnac(seed)
MCC	0.495	>	0.194
Average MCC ± 95% Confidence Intervals	0.507 ± 0.174	>	0.116 ± 0.186
Sensitivity	0.379	>	0.038
Positive Predictive Value	0.657	<	1.000
Total TP	140	>	14
Total TN	32442	<	32641
Total FP	75	>	0
Total FP CONTRA	5	>	0
Total FP INCONS	68	>	0
Total FP COMP	2	>	0
Total FN	229	<	355
P-value	1.62913390836e-08

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

Total Scores
MCC	0.495
Average MCC ± 95% Confidence Intervals	0.507 ± 0.174
Sensitivity	0.379
Positive Predictive Value	0.657
Nr of predictions	12

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2KDQ_B	mir-TAR links to Rfam database...	0.95	0.91	1.00	10	396	0	0	0	0	1
2LC8_A	GP_knot1 links to Rfam database...	-0.01	0.00	0.00	0	1526	14	2	12	0	20
3A3A_A	tRNA-Sec links to Rfam database...	0.53	0.41	0.71	15	3634	6	0	6	0	22
3GX2_A	SAM links to Rfam database...	0.50	0.40	0.64	16	4346	10	1	8	1	24
3IVN_B	Purine links to Rfam database...	0.78	0.61	1.00	19	2327	0	0	0	0	12
3LA5_A	Purine links to Rfam database...	0.78	0.62	1.00	21	2464	0	0	0	0	13
3RKF_A	Purine links to Rfam database...	0.76	0.59	1.00	20	2191	0	0	0	0	14
3SD1_A	THF links to Rfam database...	0.30	0.17	0.54	7	3903	6	0	6	0	35
3W3S_B	tRNA-Sec links to Rfam database...	0.27	0.23	0.33	9	4726	18	1	17	0	31
4AOB_A	SAM links to Rfam database...	0.35	0.26	0.48	11	4348	13	1	11	1	31
4ENB_A	crcB links to Rfam database...	0.43	0.32	0.60	6	1265	4	0	4	0	13
4ENC_A	crcB links to Rfam database...	0.43	0.32	0.60	6	1316	4	0	4	0	13

Total Scores
MCC	0.194
Average MCC ± 95% Confidence Intervals	0.116 ± 0.186
Sensitivity	0.038
Positive Predictive Value	1.000
Nr of predictions	12

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2KDQ_B	mir-TAR links to Rfam database...	0.95	0.91	1.00	10	396	0	0	0	0	1
2LC8_A	GP_knot1 links to Rfam database...	0.44	0.20	1.00	4	1536	0	0	0	0	16
3A3A_A	tRNA-Sec links to Rfam database...	0.00	0.00	0.00	0	3655	0	0	0	0	37
3GX2_A	SAM links to Rfam database...	0.00	0.00	0.00	0	4371	0	0	0	0	40
3IVN_B	Purine links to Rfam database...	0.00	0.00	0.00	0	2346	0	0	0	0	31
3LA5_A	Purine links to Rfam database...	0.00	0.00	0.00	0	2485	0	0	0	0	34
3RKF_A	Purine links to Rfam database...	0.00	0.00	0.00	0	2211	0	0	0	0	34
3SD1_A	THF links to Rfam database...	0.00	0.00	0.00	0	3916	0	0	0	0	42
3W3S_B	tRNA-Sec links to Rfam database...	0.00	0.00	0.00	0	4753	0	0	0	0	40
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

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