CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	PPfold(20)		CentroidFold
MCC	0.662	>	0.487
Average MCC ± 95% Confidence Intervals	0.642 ± 0.102	>	0.511 ± 0.117
Sensitivity	0.526	>	0.413
Positive Predictive Value	0.837	>	0.581
Total TP	396	>	311
Total TN	113821	>	113759
Total FP	99	<	252
Total FP CONTRA	0	<	22
Total FP INCONS	77	<	202
Total FP COMP	22	<	28
Total FN	357	<	442
P-value	5.23657817852e-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	0.662
Average MCC ± 95% Confidence Intervals	0.642 ± 0.102
Sensitivity	0.526
Positive Predictive Value	0.837
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...	0.63	0.45	0.90	9	980	1	0	1	0	11
3AMU_B	tRNA links to Rfam database...	0.86	0.74	1.00	20	2983	1	0	0	1	7
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_7	5S_rRNA links to Rfam database...	0.74	0.61	0.89	33	7103	4	0	4	0	21
3J3E_8	5_8S_rRNA links to Rfam database...	0.14	0.09	0.23	3	7490	13	0	10	3	30
3J3F_8	5_8S_rRNA links to Rfam database...	0.33	0.25	0.43	9	12225	18	0	12	6	27
3J3F_7	5S_rRNA links to Rfam database...	0.80	0.68	0.94	34	7224	3	0	2	1	16
3RKF_A	Purine links to Rfam database...	0.73	0.56	0.95	19	2191	1	0	1	0	15
3SD1_A	THF links to Rfam database...	0.68	0.52	0.88	22	3891	3	0	3	0	20
3ZEX_C	5_8S_rRNA links to Rfam database...	0.33	0.21	0.52	11	14175	12	0	10	2	41
3ZEX_D	5S_rRNA links to Rfam database...	0.81	0.71	0.92	35	6983	3	0	3	0	14
3ZND_W	tRNA links to Rfam database...	0.47	0.43	0.53	10	2984	11	0	9	2	13
4A1C_3	5S_rRNA links to Rfam database...	0.77	0.63	0.94	34	7104	2	0	2	0	20
4A1C_2	5_8S_rRNA links to Rfam database...	0.21	0.15	0.29	5	11764	16	0	12	4	28
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...	0.56	0.37	0.88	7	1267	1	0	1	0	12
4ENC_A	crcB links to Rfam database...	0.58	0.42	0.80	8	1316	2	0	2	0	11
4FRG_B	AdoCbl-variant links to Rfam database...	0.73	0.56	0.95	18	3467	1	0	1	0	14

Total Scores
MCC	0.487
Average MCC ± 95% Confidence Intervals	0.511 ± 0.117
Sensitivity	0.413
Positive Predictive Value	0.581
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...	0.92	0.90	0.95	18	971	1	0	1	0	2
3AMU_B	tRNA links to Rfam database...	0.70	0.59	0.84	16	2984	5	0	3	2	11
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_7	5S_rRNA links to Rfam database...	0.46	0.37	0.59	20	7106	14	1	13	0	34
3J3E_8	5_8S_rRNA links to Rfam database...	0.00	0.00	0.00	0	7485	21	2	16	3	33
3J3F_8	5_8S_rRNA links to Rfam database...	0.34	0.33	0.34	12	12211	34	4	19	11	24
3J3F_7	5S_rRNA links to Rfam database...	0.20	0.18	0.23	9	7221	30	1	29	0	41
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...	0.58	0.48	0.71	20	3888	8	1	7	0	22
3ZEX_C	5_8S_rRNA links to Rfam database...	0.47	0.27	0.82	14	14179	3	1	2	0	38
3ZEX_D	5S_rRNA links to Rfam database...	0.73	0.59	0.91	29	6989	3	0	3	0	20
3ZND_W	tRNA links to Rfam database...	0.20	0.22	0.19	5	2977	23	1	20	2	18
4A1C_3	5S_rRNA links to Rfam database...	0.67	0.56	0.81	30	7103	7	1	6	0	24
4A1C_2	5_8S_rRNA links to Rfam database...	0.16	0.15	0.17	5	11752	29	5	19	5	28
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.