CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	CentroidAlifold(20)		IPknot
MCC	0.812	>	0.639
Average MCC ± 95% Confidence Intervals	0.761 ± 0.117	>	0.617 ± 0.117
Sensitivity	0.745	>	0.637
Positive Predictive Value	0.890	>	0.649
Total TP	379	>	324
Total TN	45530	>	45457
Total FP	92	<	241
Total FP CONTRA	14	<	52
Total FP INCONS	33	<	123
Total FP COMP	45	<	66
Total FN	130	<	185
P-value	5.19332990918e-08

Comparison of performance of CentroidAlifold(20) and IPknot. 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 CentroidAlifold(20) and IPknot).
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 CentroidAlifold(20) and IPknot).
Comparison of average Matthews Correlation Coefficients (MCCs) for CentroidAlifold(20) and IPknot. 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 CentroidAlifold(20) and IPknot).

Total Scores
MCC	0.812
Average MCC ± 95% Confidence Intervals	0.761 ± 0.117
Sensitivity	0.745
Positive Predictive Value	0.890
Nr of predictions	21

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
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	2	1	0	1	1
3J2L_3	5S_rRNA links to Rfam database...	0.94	0.88	1.00	30	2990	3	0	0	3	4
3J3D_C	tRNA links to Rfam database...	0.90	0.95	0.86	18	947	3	3	0	0	1
3J3E_8	5_8S_rRNA links to Rfam database...	0.00	0.00	0.00	0	2738	4	1	3	0	15
3J3E_7	5S_rRNA links to Rfam database...	0.80	0.82	0.78	28	2705	12	1	7	4	6
3J3F_8	5_8S_rRNA links to Rfam database...	0.44	0.37	0.54	7	4748	8	3	3	2	12
3J3F_7	5S_rRNA links to Rfam database...	0.94	0.94	0.94	34	2898	4	1	1	2	2
3J3V_B	5S_rRNA links to Rfam database...	0.86	0.81	0.92	22	2632	7	0	2	5	5
3RKF_A	Purine links to Rfam database...	0.86	0.75	1.00	18	848	0	0	0	0	6
3SD1_A	THF links to Rfam database...	0.85	0.76	0.96	22	1510	1	0	1	0	7
3ZEX_D	5S_rRNA links to Rfam database...	0.91	0.89	0.94	31	2763	6	0	2	4	4
3ZEX_C	5_8S_rRNA links to Rfam database...	0.44	0.31	0.64	9	5360	7	1	4	2	20
3ZND_W	tRNA links to Rfam database...	0.67	0.75	0.60	6	1181	16	0	4	12	2
4A1C_3	5S_rRNA links to Rfam database...	0.93	0.92	0.94	34	2727	4	0	2	2	3
4A1C_2	5_8S_rRNA links to Rfam database...	0.33	0.25	0.45	5	4505	8	3	3	2	15
4AOB_A	SAM links to Rfam database...	0.89	0.79	1.00	23	1414	2	0	0	2	6
4ENB_A	crcB links to Rfam database...	0.77	0.60	1.00	9	463	0	0	0	0	6
4ENC_A	crcB links to Rfam database...	0.68	0.47	1.00	7	489	0	0	0	0	8
4FRG_B	AdoCbl-variant links to Rfam database...	0.81	0.71	0.94	17	1184	2	0	1	1	7

Total Scores
MCC	0.639
Average MCC ± 95% Confidence Intervals	0.617 ± 0.117
Sensitivity	0.637
Positive Predictive Value	0.649
Nr of predictions	21

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
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	1	0	0	1	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...	0.82	0.82	0.82	28	2986	10	0	6	4	6
3J3D_C	tRNA links to Rfam database...	0.52	0.53	0.53	10	949	9	3	6	0	9
3J3E_8	5_8S_rRNA links to Rfam database...	-0.01	0.00	0.00	0	2723	25	5	14	6	15
3J3E_7	5S_rRNA links to Rfam database...	0.60	0.56	0.66	19	2712	11	1	9	1	15
3J3F_8	5_8S_rRNA links to Rfam database...	0.36	0.47	0.28	9	4729	40	11	12	17	10
3J3F_7	5S_rRNA links to Rfam database...	0.81	0.83	0.79	30	2896	10	1	7	2	6
3J3V_B	5S_rRNA links to Rfam database...	0.54	0.56	0.54	15	2628	16	4	9	3	12
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...	0.74	0.69	0.80	20	1508	5	0	5	0	9
3ZEX_D	5S_rRNA links to Rfam database...	0.81	0.80	0.82	28	2762	10	0	6	4	7
3ZEX_C	5_8S_rRNA links to Rfam database...	0.51	0.34	0.77	10	5361	7	1	2	4	19
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...	0.83	0.81	0.86	30	2728	7	0	5	2	7
4A1C_2	5_8S_rRNA links to Rfam database...	0.23	0.25	0.22	5	4493	26	8	10	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	0	0	0	0	4
4ENC_A	crcB links to Rfam database...	0.59	0.53	0.67	8	484	4	0	4	0	7
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.