CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	Carnac(20)		RNAshapes
MCC	0.641	>	0.576
Average MCC ± 95% Confidence Intervals	0.582 ± 0.134	>	0.564 ± 0.126
Sensitivity	0.456	<	0.596
Positive Predictive Value	0.908	>	0.564
Total TP	265	<	346
Total TN	68237	>	67915
Total FP	41	<	359
Total FP CONTRA	11	<	80
Total FP INCONS	16	<	188
Total FP COMP	14	<	91
Total FN	316	>	235
P-value	4.98172311752e-08

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

Total Scores
MCC	0.641
Average MCC ± 95% Confidence Intervals	0.582 ± 0.134
Sensitivity	0.456
Positive Predictive Value	0.908
Nr of predictions	21

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
3J20_0	tRNA links to Rfam database...	0.69	0.71	0.68	15	1197	8	1	6	1	6
3J3D_C	tRNA links to Rfam database...	0.90	0.95	0.86	18	947	3	3	0	0	1
3J3E_8	5_8S_rRNA links to Rfam database...	0.00	0.00	0.00	0	2742	0	0	0	0	15
3J3F_8	5_8S_rRNA links to Rfam database...	0.61	0.37	1.00	7	4754	2	0	0	2	12
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
3ZEX_C	5_8S_rRNA links to Rfam database...	0.37	0.21	0.67	6	5365	4	1	2	1	23
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
4FRG_B	AdoCbl-variant links to Rfam database...	0.50	0.25	1.00	6	1196	0	0	0	0	18

Total Scores
MCC	0.576
Average MCC ± 95% Confidence Intervals	0.564 ± 0.126
Sensitivity	0.596
Positive Predictive Value	0.564
Nr of predictions	21

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...	0.91	0.89	0.93	25	1422	3	1	1	1	3
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...	0.57	0.58	0.56	55	25437	50	16	28	6	40
3J20_0	tRNA links to Rfam database...	0.51	0.57	0.48	12	1194	14	3	10	1	9
3J3D_C	tRNA links to Rfam database...	0.63	0.68	0.59	13	946	9	3	6	0	6
3J3E_8	5_8S_rRNA links to Rfam database...	0.26	0.33	0.21	5	2718	29	6	13	10	10
3J3F_8	5_8S_rRNA links to Rfam database...	0.33	0.42	0.26	8	4730	42	11	12	19	11
3JYV_7	tRNA links to Rfam database...	-0.02	0.00	0.00	0	1092	20	1	18	1	20
3LA5_A	Purine links to Rfam database...	0.89	0.80	1.00	20	934	0	0	0	0	5
3NPB_A	SAM links to Rfam database...	0.84	0.76	0.93	28	2248	5	1	1	3	9
3O58_3	5_8S_rRNA links to Rfam database...	0.41	0.50	0.34	11	4732	38	6	15	17	11
3PDR_A	ykoK links to Rfam database...	0.80	0.80	0.80	40	4790	12	3	7	2	10
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...	0.77	0.76	0.79	22	1505	6	4	2	0	7
3ZEX_C	5_8S_rRNA links to Rfam database...	0.29	0.34	0.26	10	5335	42	5	24	13	19
4A1C_2	5_8S_rRNA links to Rfam database...	0.19	0.25	0.16	5	4484	41	11	16	14	15
4AOB_A	SAM links to Rfam database...	0.60	0.59	0.63	17	1410	11	4	6	1	12
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...	0.37	0.33	0.45	5	485	7	0	6	1	10
4FRG_B	AdoCbl-variant links to Rfam database...	0.36	0.38	0.38	9	1178	15	2	13	0	15

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