CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	PETfold_pre2.0(20)		RNAshapes
MCC	0.793	>	0.564
Average MCC ± 95% Confidence Intervals	0.752 ± 0.129	>	0.546 ± 0.133
Sensitivity	0.776	>	0.600
Positive Predictive Value	0.815	>	0.540
Total TP	339	>	262
Total TN	41984	>	41915
Total FP	145	<	314
Total FP CONTRA	14	<	60
Total FP INCONS	63	<	163
Total FP COMP	68	<	91
Total FN	98	<	175
P-value	2.9966815982e-08

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

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_8	5_8S_rRNA links to Rfam database...	0.34	0.37	0.32	7	4739	24	5	10	9	12
3J3F_7	5S_rRNA links to Rfam database...	0.93	0.92	0.94	33	2899	6	0	2	4	3
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	0.564
Average MCC ± 95% Confidence Intervals	0.546 ± 0.133
Sensitivity	0.600
Positive Predictive Value	0.540
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...	0.51	0.57	0.48	12	1194	14	3	10	1	9
3J2L_3	5S_rRNA links to Rfam database...	0.77	0.79	0.75	27	2984	14	1	8	5	7
3J3D_C	tRNA links to Rfam database...	0.63	0.68	0.59	13	946	9	3	6	0	6
3J3E_8	5_8S_rRNA links to Rfam database...	0.26	0.33	0.21	5	2718	29	6	13	10	10
3J3E_7	5S_rRNA links to Rfam database...	0.64	0.65	0.65	22	2707	16	1	11	4	12
3J3F_8	5_8S_rRNA links to Rfam database...	0.33	0.42	0.26	8	4730	42	11	12	19	11
3J3F_7	5S_rRNA links to Rfam database...	0.83	0.81	0.85	29	2900	7	0	5	2	7
3J3V_B	5S_rRNA links to Rfam database...	0.23	0.26	0.23	7	2625	27	4	20	3	20
3ZEX_D	5S_rRNA links to Rfam database...	0.86	0.80	0.93	28	2766	6	0	2	4	7
3ZEX_C	5_8S_rRNA links to Rfam database...	0.29	0.34	0.26	10	5335	42	5	24	13	19
3ZND_W	tRNA links to Rfam database...	0.24	0.38	0.16	3	1172	24	9	7	8	5
4A1C_2	5_8S_rRNA links to Rfam database...	0.19	0.25	0.16	5	4484	41	11	16	14	15
4A1C_3	5S_rRNA links to Rfam database...	0.86	0.84	0.89	31	2728	7	0	4	3	6
4AOB_A	SAM links to Rfam database...	0.60	0.59	0.63	17	1410	11	4	6	1	12
4ENB_A	crcB links to Rfam database...	0.85	0.73	1.00	11	461	2	0	0	2	4
4ENC_A	crcB links to Rfam database...	0.37	0.33	0.45	5	485	7	0	6	1	10
4FRG_B	AdoCbl-variant links to Rfam database...	0.36	0.38	0.38	9	1178	15	2	13	0	15

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