CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	CentroidAlifold(20)		CMfinder(20)
MCC	0.822	>	0.648
Average MCC ± 95% Confidence Intervals	0.748 ± 0.196	>	0.625 ± 0.138
Sensitivity	0.783	>	0.563
Positive Predictive Value	0.866	>	0.754
Total TP	213	>	153
Total TN	25984	<	26027
Total FP	67	<	71
Total FP CONTRA	10	<	15
Total FP INCONS	23	<	35
Total FP COMP	34	>	21
Total FN	59	<	119
P-value	1.50834591464e-08

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

Total Scores
MCC	0.822
Average MCC ± 95% Confidence Intervals	0.748 ± 0.196
Sensitivity	0.783
Positive Predictive Value	0.866
Nr of predictions	11

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
3J20_0	tRNA links to Rfam database...	0.95	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
3ZEX_D	5S_rRNA links to Rfam database...	0.91	0.89	0.94	31	2763	6	0	2	4	4
3ZND_W	tRNA links to Rfam database...	0.67	0.75	0.60	6	1181	16	0	4	12	2
4FRG_B	AdoCbl-variant links to Rfam database...	0.81	0.71	0.94	17	1184	2	0	1	1	7

Total Scores
MCC	0.648
Average MCC ± 95% Confidence Intervals	0.625 ± 0.138
Sensitivity	0.563
Positive Predictive Value	0.754
Nr of predictions	11

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	0.76	0.94	16	1202	2	1	0	1	5
3J2L_3	5S_rRNA links to Rfam database...	0.57	0.50	0.65	17	2994	11	2	7	2	17
3J3D_C	tRNA links to Rfam database...	0.81	0.79	0.83	15	950	3	3	0	0	4
3J3E_8	5_8S_rRNA links to Rfam database...	0.14	0.13	0.17	2	2730	10	3	7	0	13
3J3E_7	5S_rRNA links to Rfam database...	0.81	0.74	0.89	25	2713	5	0	3	2	9
3J3F_8	5_8S_rRNA links to Rfam database...	0.48	0.47	0.50	9	4743	11	5	4	2	10
3J3F_7	5S_rRNA links to Rfam database...	0.79	0.72	0.87	26	2904	6	1	3	2	10
3J3V_B	5S_rRNA links to Rfam database...	0.53	0.41	0.69	11	2640	6	0	5	1	16
3ZEX_D	5S_rRNA links to Rfam database...	0.70	0.54	0.90	19	2775	3	0	2	1	16
3ZND_W	tRNA links to Rfam database...	0.67	0.75	0.60	6	1181	14	0	4	10	2
4FRG_B	AdoCbl-variant links to Rfam database...	0.54	0.29	1.00	7	1195	0	0	0	0	17

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