CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	PETfold_pre2.0(20)		RNAwolf
MCC	0.793	>	0.392
Average MCC ± 95% Confidence Intervals	0.752 ± 0.129	>	0.413 ± 0.120
Sensitivity	0.776	>	0.410
Positive Predictive Value	0.815	>	0.387
Total TP	339	>	179
Total TN	41984	>	41938
Total FP	145	<	353
Total FP CONTRA	14	<	75
Total FP INCONS	63	<	208
Total FP COMP	68	<	70
Total FN	98	<	258
P-value	3.27388928538e-08

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

Total Scores
MCC	0.793
Average MCC ± 95% Confidence Intervals	0.752 ± 0.129
Sensitivity	0.776
Positive Predictive Value	0.815
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...	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_8	5_8S_rRNA links to Rfam database...	0.48	0.47	0.50	7	2728	11	2	5	4	8
3J3E_7	5S_rRNA links to Rfam database...	0.94	0.94	0.94	32	2707	7	0	2	5	2
3J3F_7	5S_rRNA links to Rfam database...	0.93	0.92	0.94	33	2899	6	0	2	4	3
3J3F_8	5_8S_rRNA links to Rfam database...	0.34	0.37	0.32	7	4739	24	5	10	9	12
3J3V_B	5S_rRNA links to Rfam database...	0.90	0.89	0.92	24	2630	11	0	2	9	3
3ZEX_D	5S_rRNA links to Rfam database...	0.93	0.91	0.94	32	2762	6	0	2	4	3
3ZEX_C	5_8S_rRNA links to Rfam database...	0.26	0.24	0.29	7	5350	20	1	16	3	22
3ZND_W	tRNA links to Rfam database...	0.67	0.75	0.60	6	1181	15	0	4	11	2
4A1C_2	5_8S_rRNA links to Rfam database...	0.25	0.25	0.25	5	4496	25	2	13	10	15
4A1C_3	5S_rRNA links to Rfam database...	1.00	1.00	1.00	37	2726	1	0	0	1	0
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...	0.68	0.53	0.89	8	463	1	0	1	0	7
4ENC_A	crcB links to Rfam database...	0.61	0.53	0.73	8	485	3	0	3	0	7
4FRG_B	AdoCbl-variant links to Rfam database...	0.89	0.83	0.95	20	1181	2	0	1	1	4

Total Scores
MCC	0.392
Average MCC ± 95% Confidence Intervals	0.413 ± 0.120
Sensitivity	0.410
Positive Predictive Value	0.387
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...	0.53	0.55	0.52	11	1091	11	4	6	1	9
3J20_0	tRNA links to Rfam database...	0.54	0.57	0.52	12	1196	12	2	9	1	9
3J2L_3	5S_rRNA links to Rfam database...	0.71	0.71	0.73	24	2987	13	1	8	4	10
3J3D_C	tRNA links to Rfam database...	0.92	0.95	0.90	18	948	3	2	0	1	1
3J3E_8	5_8S_rRNA links to Rfam database...	-0.01	0.00	0.00	0	2719	37	6	17	14	15
3J3E_7	5S_rRNA links to Rfam database...	0.57	0.56	0.59	19	2709	15	1	12	2	15
3J3F_7	5S_rRNA links to Rfam database...	0.27	0.28	0.28	10	2898	27	4	22	1	26
3J3F_8	5_8S_rRNA links to Rfam database...	0.28	0.37	0.23	7	4730	39	9	15	15	12
3J3V_B	5S_rRNA links to Rfam database...	0.59	0.59	0.59	16	2629	16	1	10	5	11
3ZEX_D	5S_rRNA links to Rfam database...	0.26	0.26	0.27	9	2763	24	8	16	0	26
3ZEX_C	5_8S_rRNA links to Rfam database...	0.08	0.10	0.07	3	5328	43	18	25	0	26
3ZND_W	tRNA links to Rfam database...	0.67	0.75	0.60	6	1181	15	0	4	11	2
4A1C_2	5_8S_rRNA links to Rfam database...	0.12	0.15	0.10	3	4487	38	12	14	12	17
4A1C_3	5S_rRNA links to Rfam database...	0.32	0.30	0.35	11	2732	21	1	19	1	26
4AOB_A	SAM links to Rfam database...	0.26	0.24	0.30	7	1414	17	2	14	1	22
4ENB_A	crcB links to Rfam database...	0.45	0.40	0.55	6	461	5	1	4	0	9
4ENC_A	crcB links to Rfam database...	0.34	0.33	0.38	5	483	9	0	8	1	10
4FRG_B	AdoCbl-variant links to Rfam database...	0.54	0.50	0.60	12	1182	8	3	5	0	12

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