CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	PETfold_pre2.0(20)		CentroidFold
MCC	0.649	>	0.445
Average MCC ± 95% Confidence Intervals	0.630 ± 0.114	>	0.457 ± 0.120
Sensitivity	0.530	>	0.376
Positive Predictive Value	0.798	>	0.533
Total TP	364	>	258
Total TN	110739	>	110711
Total FP	120	<	252
Total FP CONTRA	4	<	22
Total FP INCONS	88	<	204
Total FP COMP	28	>	26
Total FN	323	<	429
P-value	2.91763127434e-08

Comparison of performance of PETfold_pre2.0(20) and CentroidFold. 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 PETfold_pre2.0(20) and CentroidFold).
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 PETfold_pre2.0(20) and CentroidFold).
Comparison of average Matthews Correlation Coefficients (MCCs) for PETfold_pre2.0(20) and CentroidFold. 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 PETfold_pre2.0(20) and CentroidFold).

Total Scores
MCC	0.649
Average MCC ± 95% Confidence Intervals	0.630 ± 0.114
Sensitivity	0.530
Positive Predictive Value	0.798
Nr of predictions	18

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
3J20_1	tRNA links to Rfam database...	0.96	0.91	1.00	21	2905	0	0	0	0	2
3J20_0	tRNA links to Rfam database...	0.84	0.70	1.00	21	2829	0	0	0	0	9
3J2L_3	5S_rRNA links to Rfam database...	0.78	0.62	0.97	33	7841	3	0	1	2	20
3J3D_C	tRNA links to Rfam database...	0.80	0.68	0.95	19	2755	1	0	1	0	9
3J3E_8	5_8S_rRNA links to Rfam database...	0.32	0.21	0.50	7	7489	11	0	7	4	26
3J3E_7	5S_rRNA links to Rfam database...	0.74	0.63	0.87	34	7101	5	1	4	0	20
3J3F_7	5S_rRNA links to Rfam database...	0.78	0.68	0.89	34	7222	5	1	3	1	16
3J3F_8	5_8S_rRNA links to Rfam database...	0.30	0.25	0.38	9	12222	22	0	15	7	27
3J3V_B	5S_rRNA links to Rfam database...	0.65	0.51	0.83	29	6986	6	1	5	0	28
3ZEX_D	5S_rRNA links to Rfam database...	0.81	0.71	0.92	35	6983	3	0	3	0	14
3ZEX_C	5_8S_rRNA links to Rfam database...	0.24	0.17	0.35	9	14170	18	0	17	1	43
3ZND_W	tRNA links to Rfam database...	0.47	0.43	0.53	10	2984	11	0	9	2	13
4A1C_2	5_8S_rRNA links to Rfam database...	0.19	0.15	0.25	5	11761	25	0	15	10	28
4A1C_3	5S_rRNA links to Rfam database...	0.82	0.69	0.97	37	7102	1	0	1	0	17
4AOB_A	SAM links to Rfam database...	0.74	0.60	0.93	25	4344	3	0	2	1	17
4ENB_A	crcB links to Rfam database...	0.61	0.42	0.89	8	1266	1	0	1	0	11
4ENC_A	crcB links to Rfam database...	0.55	0.42	0.73	8	1315	3	0	3	0	11
4FRG_B	AdoCbl-variant links to Rfam database...	0.75	0.63	0.91	20	3464	2	1	1	0	12

Total Scores
MCC	0.445
Average MCC ± 95% Confidence Intervals	0.457 ± 0.120
Sensitivity	0.376
Positive Predictive Value	0.533
Nr of predictions	18

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
3J20_1	tRNA links to Rfam database...	0.91	0.87	0.95	20	2905	2	0	1	1	3
3J20_0	tRNA links to Rfam database...	0.44	0.40	0.50	12	2826	13	0	12	1	18
3J2L_3	5S_rRNA links to Rfam database...	0.53	0.49	0.58	26	7830	21	0	19	2	27
3J3D_C	tRNA links to Rfam database...	0.49	0.43	0.57	12	2754	9	0	9	0	16
3J3E_8	5_8S_rRNA links to Rfam database...	0.00	0.00	0.00	0	7485	21	2	16	3	33
3J3E_7	5S_rRNA links to Rfam database...	0.46	0.37	0.59	20	7106	14	1	13	0	34
3J3F_7	5S_rRNA links to Rfam database...	0.20	0.18	0.23	9	7221	30	1	29	0	41
3J3F_8	5_8S_rRNA links to Rfam database...	0.34	0.33	0.34	12	12211	34	4	19	11	24
3J3V_B	5S_rRNA links to Rfam database...	0.47	0.37	0.60	21	6986	14	1	13	0	36
3ZEX_D	5S_rRNA links to Rfam database...	0.73	0.59	0.91	29	6989	3	0	3	0	20
3ZEX_C	5_8S_rRNA links to Rfam database...	0.47	0.27	0.82	14	14179	3	1	2	0	38
3ZND_W	tRNA links to Rfam database...	0.20	0.22	0.19	5	2977	23	1	20	2	18
4A1C_2	5_8S_rRNA links to Rfam database...	0.16	0.15	0.17	5	11752	29	5	19	5	28
4A1C_3	5S_rRNA links to Rfam database...	0.67	0.56	0.81	30	7103	7	1	6	0	24
4AOB_A	SAM links to Rfam database...	0.45	0.33	0.61	14	4348	10	1	8	1	28
4ENB_A	crcB links to Rfam database...	0.76	0.58	1.00	11	1264	0	0	0	0	8
4ENC_A	crcB links to Rfam database...	0.73	0.58	0.92	11	1314	1	1	0	0	8
4FRG_B	AdoCbl-variant links to Rfam database...	0.24	0.22	0.28	7	3461	18	3	15	0	25

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