CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	CentroidAlifold(20)		RNASLOpt
MCC	0.798	>	0.559
Average MCC ± 95% Confidence Intervals	0.738 ± 0.134	>	0.566 ± 0.141
Sensitivity	0.732	>	0.561
Positive Predictive Value	0.874	>	0.566
Total TP	320	>	245
Total TN	42034	>	41967
Total FP	89	<	266
Total FP CONTRA	14	<	63
Total FP INCONS	32	<	125
Total FP COMP	43	<	78
Total FN	117	<	192
P-value	3.05041766982e-08

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

Total Scores
MCC	0.798
Average MCC ± 95% Confidence Intervals	0.738 ± 0.134
Sensitivity	0.732
Positive Predictive Value	0.874
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	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_7	5S_rRNA links to Rfam database...	0.94	0.94	0.94	34	2898	4	1	1	2	2
3J3F_8	5_8S_rRNA links to Rfam database...	0.44	0.37	0.54	7	4748	8	3	3	2	12
3J3V_B	5S_rRNA links to Rfam database...	0.86	0.81	0.92	22	2632	7	0	2	5	5
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_2	5_8S_rRNA links to Rfam database...	0.33	0.25	0.45	5	4505	8	3	3	2	15
4A1C_3	5S_rRNA links to Rfam database...	0.93	0.92	0.94	34	2727	4	0	2	2	3
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	0.559
Average MCC ± 95% Confidence Intervals	0.566 ± 0.141
Sensitivity	0.561
Positive Predictive Value	0.566
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...	0.74	0.76	0.73	16	1197	7	3	3	1	5
3J2L_3	5S_rRNA links to Rfam database...	0.71	0.68	0.74	23	2989	11	0	8	3	11
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...	-0.01	0.00	0.00	0	2724	30	6	12	12	15
3J3E_7	5S_rRNA links to Rfam database...	0.61	0.56	0.68	19	2713	10	1	8	1	15
3J3F_7	5S_rRNA links to Rfam database...	0.21	0.22	0.22	8	2898	28	3	25	0	28
3J3F_8	5_8S_rRNA links to Rfam database...	0.39	0.47	0.32	9	4733	38	10	9	19	10
3J3V_B	5S_rRNA links to Rfam database...	0.60	0.59	0.62	16	2630	14	2	8	4	11
3ZEX_D	5S_rRNA links to Rfam database...	0.86	0.74	1.00	26	2770	4	0	0	4	9
3ZEX_C	5_8S_rRNA links to Rfam database...	0.32	0.34	0.31	10	5342	36	8	14	14	19
3ZND_W	tRNA links to Rfam database...	0.26	0.38	0.19	3	1175	22	7	6	9	5
4A1C_2	5_8S_rRNA links to Rfam database...	0.30	0.40	0.24	8	4482	35	13	13	9	12
4A1C_3	5S_rRNA links to Rfam database...	0.79	0.73	0.87	27	2732	5	0	4	1	10
4AOB_A	SAM links to Rfam database...	0.31	0.28	0.38	8	1416	13	3	10	0	21
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...	0.73	0.60	0.90	9	486	1	1	0	0	6
4FRG_B	AdoCbl-variant links to Rfam database...	0.60	0.58	0.64	14	1180	8	3	5	0	10

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