CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	RSpredict(20)		CMfinder(20)
MCC	0.688	>	0.660
Average MCC ± 95% Confidence Intervals	0.615 ± 0.235	<	0.635 ± 0.153
Sensitivity	0.653	>	0.580
Positive Predictive Value	0.731	<	0.759
Total TP	160	>	142
Total TN	23355	<	23387
Total FP	90	>	65
Total FP CONTRA	20	>	15
Total FP INCONS	39	>	30
Total FP COMP	31	>	20
Total FN	85	<	103
P-value	6.62909925123e-09

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

Total Scores
MCC	0.688
Average MCC ± 95% Confidence Intervals	0.615 ± 0.235
Sensitivity	0.653
Positive Predictive Value	0.731
Nr of predictions	10

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
3J20_0	tRNA links to Rfam database...	0.90	0.90	0.90	19	1198	3	1	1	1	2
3J2L_3	5S_rRNA links to Rfam database...	0.71	0.59	0.87	20	2997	6	0	3	3	14
3J3D_C	tRNA links to Rfam database...	0.82	0.84	0.80	16	948	4	3	1	0	3
3J3E_8	5_8S_rRNA links to Rfam database...	-0.01	0.00	0.00	0	2724	19	5	13	1	15
3J3E_7	5S_rRNA links to Rfam database...	0.82	0.79	0.84	27	2709	7	0	5	2	7
3J3F_8	5_8S_rRNA links to Rfam database...	0.42	0.47	0.38	9	4737	26	9	6	11	10
3J3F_7	5S_rRNA links to Rfam database...	0.94	0.94	0.94	34	2898	3	1	1	1	2
3ZEX_D	5S_rRNA links to Rfam database...	0.88	0.83	0.94	29	2765	7	0	2	5	6
3ZND_W	tRNA links to Rfam database...	0.47	0.38	0.60	3	1186	9	0	2	7	5
4FRG_B	AdoCbl-variant links to Rfam database...	0.19	0.13	0.33	3	1193	6	1	5	0	21

Total Scores
MCC	0.660
Average MCC ± 95% Confidence Intervals	0.635 ± 0.153
Sensitivity	0.580
Positive Predictive Value	0.759
Nr of predictions	10

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
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.