CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	CMfinder(20)		RNAwolf
MCC	0.648	>	0.470
Average MCC ± 95% Confidence Intervals	0.625 ± 0.138	>	0.486 ± 0.175
Sensitivity	0.563	>	0.489
Positive Predictive Value	0.754	>	0.462
Total TP	153	>	133
Total TN	26027	>	25942
Total FP	71	<	209
Total FP CONTRA	15	<	37
Total FP INCONS	35	<	118
Total FP COMP	21	<	54
Total FN	119	<	139
P-value	1.66062906821e-08

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

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

Total Scores
MCC	0.470
Average MCC ± 95% Confidence Intervals	0.486 ± 0.175
Sensitivity	0.489
Positive Predictive Value	0.462
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...	0.54	0.57	0.52	12	1196	12	2	9	1	9
3J2L_3	5S_rRNA links to Rfam database...	0.71	0.71	0.73	24	2987	13	1	8	4	10
3J3D_C	tRNA links to Rfam database...	0.92	0.95	0.90	18	948	3	2	0	1	1
3J3E_8	5_8S_rRNA links to Rfam database...	-0.01	0.00	0.00	0	2719	37	6	17	14	15
3J3E_7	5S_rRNA links to Rfam database...	0.57	0.56	0.59	19	2709	15	1	12	2	15
3J3F_8	5_8S_rRNA links to Rfam database...	0.28	0.37	0.23	7	4730	39	9	15	15	12
3J3F_7	5S_rRNA links to Rfam database...	0.27	0.28	0.28	10	2898	27	4	22	1	26
3J3V_B	5S_rRNA links to Rfam database...	0.59	0.59	0.59	16	2629	16	1	10	5	11
3ZEX_D	5S_rRNA links to Rfam database...	0.26	0.26	0.27	9	2763	24	8	16	0	26
3ZND_W	tRNA links to Rfam database...	0.67	0.75	0.60	6	1181	15	0	4	11	2
4FRG_B	AdoCbl-variant links to Rfam database...	0.54	0.50	0.60	12	1182	8	3	5	0	12

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