CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	PETfold_pre2.0(seed)		PETfold_pre2.0(20)
MCC	0.674	>	0.632
Average MCC ± 95% Confidence Intervals	0.691 ± 0.074	>	0.629 ± 0.108
Sensitivity	0.538	>	0.497
Positive Predictive Value	0.846	>	0.806
Total TP	615	>	568
Total TN	539669	<	539691
Total FP	141	<	166
Total FP CONTRA	10	>	9
Total FP INCONS	102	<	128
Total FP COMP	29	=	29
Total FN	529	<	576
P-value	3.10499527239e-08

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

Total Scores
MCC	0.674
Average MCC ± 95% Confidence Intervals	0.691 ± 0.074
Sensitivity	0.538
Positive Predictive Value	0.846
Nr of predictions	19

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
3J20_0	tRNA links to Rfam database...	0.84	0.70	1.00	21	2829	1	0	0	1	9
3J20_1	tRNA links to Rfam database...	0.96	0.91	1.00	21	2905	1	0	0	1	2
3J2C_N	SSU_rRNA_bacteria links to Rfam database...	0.60	0.45	0.80	205	428945	53	6	45	2	252
3J2L_3	5S_rRNA links to Rfam database...	0.77	0.62	0.94	33	7840	4	0	2	2	20
3J3D_C	tRNA links to Rfam database...	0.82	0.71	0.95	20	2754	2	0	1	1	8
3J3E_8	5_8S_rRNA links to Rfam database...	0.43	0.30	0.63	10	7487	8	0	6	2	23
3J3E_7	5S_rRNA links to Rfam database...	0.78	0.67	0.92	36	7101	3	0	3	0	18
3J3F_8	5_8S_rRNA links to Rfam database...	0.63	0.53	0.76	19	12221	10	0	6	4	17
3J3F_7	5S_rRNA links to Rfam database...	0.85	0.74	0.97	37	7222	2	0	1	1	13
3J3V_B	5S_rRNA links to Rfam database...	0.76	0.61	0.95	35	6984	3	0	2	1	22
3ZEX_D	5S_rRNA links to Rfam database...	0.82	0.73	0.92	36	6982	3	0	3	0	13
3ZEX_C	5_8S_rRNA links to Rfam database...	0.53	0.37	0.76	19	14171	10	1	5	4	33
3ZND_W	tRNA links to Rfam database...	0.47	0.43	0.53	10	2984	12	0	9	3	13
4A1C_2	5_8S_rRNA links to Rfam database...	0.57	0.45	0.71	15	11760	12	0	6	6	18
4A1C_3	5S_rRNA links to Rfam database...	0.83	0.70	0.97	38	7101	1	0	1	0	16
4AOB_A	SAM links to Rfam database...	0.72	0.57	0.92	24	4345	3	0	2	1	18
4ENB_A	crcB links to Rfam database...	0.50	0.42	0.62	8	1262	5	1	4	0	11
4ENC_A	crcB links to Rfam database...	0.50	0.42	0.62	8	1313	5	1	4	0	11
4FRG_B	AdoCbl-variant links to Rfam database...	0.74	0.63	0.87	20	3463	3	1	2	0	12

Total Scores
MCC	0.632
Average MCC ± 95% Confidence Intervals	0.629 ± 0.108
Sensitivity	0.497
Positive Predictive Value	0.806
Nr of predictions	19

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
3J20_0	tRNA links to Rfam database...	0.84	0.70	1.00	21	2829	0	0	0	0	9
3J20_1	tRNA links to Rfam database...	0.96	0.91	1.00	21	2905	0	0	0	0	2
3J2C_N	SSU_rRNA_bacteria links to Rfam database...	0.60	0.45	0.82	204	428952	46	5	40	1	253
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_8	5_8S_rRNA links to Rfam database...	0.30	0.25	0.38	9	12222	22	0	15	7	27
3J3F_7	5S_rRNA links to Rfam database...	0.78	0.68	0.89	34	7222	5	1	3	1	16
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

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