CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	PPfold(20)		CentroidFold
MCC	0.793	>	0.671
Average MCC ± 95% Confidence Intervals	0.749 ± 0.114	>	0.660 ± 0.116
Sensitivity	0.752	>	0.674
Positive Predictive Value	0.841	>	0.675
Total TP	376	>	337
Total TN	43210	>	43158
Total FP	119	<	228
Total FP CONTRA	14	<	55
Total FP INCONS	57	<	107
Total FP COMP	48	<	66
Total FN	124	<	163
P-value	4.94031556815e-08

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

Total Scores
MCC	0.793
Average MCC ± 95% Confidence Intervals	0.749 ± 0.114
Sensitivity	0.752
Positive Predictive Value	0.841
Nr of predictions	21

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...	0.66	0.50	0.90	9	347	1	0	1	0	9
3AMU_B	tRNA links to Rfam database...	1.00	1.00	1.00	19	1138	2	0	0	2	0
3J20_1	tRNA links to Rfam database...	1.00	1.00	1.00	20	1092	1	0	0	1	0
3J20_0	tRNA links to Rfam database...	0.95	0.95	0.95	20	1198	1	1	0	0	1
3J2L_3	5S_rRNA links to Rfam database...	0.97	0.94	1.00	32	2988	4	0	0	4	2
3J3D_C	tRNA links to Rfam database...	0.87	0.89	0.85	17	948	3	3	0	0	2
3J3E_7	5S_rRNA links to Rfam database...	0.94	0.94	0.94	32	2707	5	0	2	3	2
3J3E_8	5_8S_rRNA links to Rfam database...	0.21	0.20	0.23	3	2729	13	2	8	3	12
3J3F_8	5_8S_rRNA links to Rfam database...	0.37	0.37	0.37	7	4742	20	5	7	8	12
3J3F_7	5S_rRNA links to Rfam database...	0.93	0.92	0.94	33	2899	4	0	2	2	3
3RKF_A	Purine links to Rfam database...	0.86	0.79	0.95	19	846	1	0	1	0	5
3SD1_A	THF links to Rfam database...	0.81	0.76	0.88	22	1508	3	2	1	0	7
3ZEX_C	5_8S_rRNA links to Rfam database...	0.38	0.31	0.47	9	5355	14	0	10	4	20
3ZEX_D	5S_rRNA links to Rfam database...	0.93	0.91	0.94	32	2762	6	0	2	4	3
3ZND_W	tRNA links to Rfam database...	0.67	0.75	0.60	6	1181	15	0	4	11	2
4A1C_3	5S_rRNA links to Rfam database...	0.93	0.92	0.94	34	2727	2	0	2	0	3
4A1C_2	5_8S_rRNA links to Rfam database...	0.27	0.25	0.29	5	4499	16	1	11	4	15
4AOB_A	SAM links to Rfam database...	0.87	0.83	0.92	24	1411	4	0	2	2	5
4ENB_A	crcB links to Rfam database...	0.63	0.47	0.88	7	464	1	0	1	0	8
4ENC_A	crcB links to Rfam database...	0.64	0.53	0.80	8	486	2	0	2	0	7
4FRG_B	AdoCbl-variant links to Rfam database...	0.84	0.75	0.95	18	1183	1	0	1	0	6

Total Scores
MCC	0.671
Average MCC ± 95% Confidence Intervals	0.660 ± 0.116
Sensitivity	0.674
Positive Predictive Value	0.675
Nr of predictions	21

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...	0.94	0.94	0.94	17	339	2	0	1	1	1
3AMU_B	tRNA links to Rfam database...	0.81	0.79	0.83	15	1139	6	0	3	3	4
3J20_1	tRNA links to Rfam database...	1.00	1.00	1.00	20	1092	2	0	0	2	0
3J20_0	tRNA links to Rfam database...	0.54	0.57	0.52	12	1196	12	3	8	1	9
3J2L_3	5S_rRNA links to Rfam database...	0.74	0.76	0.72	26	2984	15	1	9	5	8
3J3D_C	tRNA links to Rfam database...	0.73	0.79	0.68	15	946	7	3	4	0	4
3J3E_7	5S_rRNA links to Rfam database...	0.61	0.59	0.65	20	2710	13	2	9	2	14
3J3E_8	5_8S_rRNA links to Rfam database...	0.12	0.13	0.13	2	2726	22	4	10	8	13
3J3F_8	5_8S_rRNA links to Rfam database...	0.36	0.47	0.28	9	4729	37	12	11	14	10
3J3F_7	5S_rRNA links to Rfam database...	0.84	0.86	0.82	31	2896	9	1	6	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...	0.70	0.69	0.71	20	1505	8	4	4	0	9
3ZEX_C	5_8S_rRNA links to Rfam database...	0.48	0.34	0.67	10	5359	6	1	4	1	19
3ZEX_D	5S_rRNA links to Rfam database...	0.88	0.86	0.91	30	2763	8	0	3	5	5
3ZND_W	tRNA links to Rfam database...	0.24	0.38	0.16	3	1172	25	9	7	9	5
4A1C_3	5S_rRNA links to Rfam database...	0.80	0.78	0.83	29	2728	8	0	6	2	8
4A1C_2	5_8S_rRNA links to Rfam database...	0.22	0.25	0.19	5	4490	29	9	12	8	15
4AOB_A	SAM links to Rfam database...	0.50	0.48	0.54	14	1411	13	3	9	1	15
4ENB_A	crcB links to Rfam database...	0.85	0.73	1.00	11	461	1	0	0	1	4
4ENC_A	crcB links to Rfam database...	0.85	0.73	1.00	11	485	1	0	0	1	4
4FRG_B	AdoCbl-variant links to Rfam database...	0.75	0.71	0.81	17	1181	4	3	1	0	7

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