CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	Carnac(20)		RNAsubopt
MCC	0.662	>	0.620
Average MCC ± 95% Confidence Intervals	0.610 ± 0.164	>	0.610 ± 0.161
Sensitivity	0.469	<	0.632
Positive Predictive Value	0.938	>	0.615
Total TP	213	<	287
Total TN	52036	>	51796
Total FP	24	<	222
Total FP CONTRA	6	<	66
Total FP INCONS	8	<	114
Total FP COMP	10	<	42
Total FN	241	>	167
P-value	2.8150742666e-08

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

Total Scores
MCC	0.662
Average MCC ± 95% Confidence Intervals	0.610 ± 0.164
Sensitivity	0.469
Positive Predictive Value	0.938
Nr of predictions	15

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
3A2K_C	tRNA links to Rfam database...	0.88	0.77	1.00	17	1091	0	0	0	0	5
3GX2_A	SAM links to Rfam database...	0.68	0.46	1.00	13	1436	0	0	0	0	15
3IVN_B	Purine links to Rfam database...	0.91	0.83	1.00	19	884	0	0	0	0	4
3IZ4_A	tmRNA links to Rfam database...	0.52	0.31	0.88	29	25503	4	3	1	0	66
3JYV_7	tRNA links to Rfam database...	0.81	0.70	0.93	14	1096	3	0	1	2	6
3LA5_A	Purine links to Rfam database...	0.91	0.84	1.00	21	933	0	0	0	0	4
3NPB_A	SAM links to Rfam database...	0.46	0.22	1.00	8	2270	3	0	0	3	29
3O58_3	5_8S_rRNA links to Rfam database...	0.60	0.36	1.00	8	4756	1	0	0	1	14
3PDR_A	ykoK links to Rfam database...	0.75	0.58	0.97	29	4810	3	1	0	2	21
3RKF_A	Purine links to Rfam database...	0.91	0.83	1.00	20	846	0	0	0	0	4
3SD1_A	THF links to Rfam database...	0.72	0.55	0.94	16	1516	1	0	1	0	13
4A1C_2	5_8S_rRNA links to Rfam database...	0.42	0.25	0.71	5	4509	3	0	2	1	15
4AOB_A	SAM links to Rfam database...	0.59	0.48	0.74	14	1418	6	2	3	1	15
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

Total Scores
MCC	0.620
Average MCC ± 95% Confidence Intervals	0.610 ± 0.161
Sensitivity	0.632
Positive Predictive Value	0.615
Nr of predictions	15

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
3A2K_C	tRNA links to Rfam database...	0.47	0.50	0.46	11	1084	13	3	10	0	11
3GX2_A	SAM links to Rfam database...	0.53	0.54	0.54	15	1421	14	4	9	1	13
3IVN_B	Purine links to Rfam database...	0.88	0.78	1.00	18	885	0	0	0	0	5
3IZ4_A	tmRNA links to Rfam database...	0.56	0.60	0.53	57	25429	54	26	24	4	38
3JYV_7	tRNA links to Rfam database...	-0.02	0.00	0.00	0	1090	21	4	17	0	20
3LA5_A	Purine links to Rfam database...	0.91	0.84	1.00	21	933	0	0	0	0	4
3NPB_A	SAM links to Rfam database...	0.84	0.78	0.91	29	2246	8	0	3	5	8
3O58_3	5_8S_rRNA links to Rfam database...	0.41	0.50	0.34	11	4732	35	6	15	14	11
3PDR_A	ykoK links to Rfam database...	0.90	0.90	0.90	45	4790	7	2	3	2	5
3RKF_A	Purine links to Rfam database...	0.91	0.83	1.00	20	846	0	0	0	0	4
3SD1_A	THF links to Rfam database...	0.73	0.72	0.75	21	1505	7	4	3	0	8
4A1C_2	5_8S_rRNA links to Rfam database...	0.18	0.25	0.14	5	4481	43	13	17	13	15
4AOB_A	SAM links to Rfam database...	0.62	0.62	0.64	18	1409	11	4	6	1	11
4ENB_A	crcB links to Rfam database...	0.85	0.73	1.00	11	461	2	0	0	2	4
4ENC_A	crcB links to Rfam database...	0.36	0.33	0.42	5	484	7	0	7	0	10

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