CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	CMfinder(20)		RNAshapes
MCC	0.521	>	0.446
Average MCC ± 95% Confidence Intervals	0.514 ± 0.127	>	0.430 ± 0.140
Sensitivity	0.366	<	0.393
Positive Predictive Value	0.748	>	0.513
Total TP	163	<	175
Total TN	67962	>	67839
Total FP	61	<	191
Total FP CONTRA	4	<	8
Total FP INCONS	51	<	158
Total FP COMP	6	<	25
Total FN	282	>	270
P-value	2.08252958266e-08

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

Total Scores
MCC	0.521
Average MCC ± 95% Confidence Intervals	0.514 ± 0.127
Sensitivity	0.366
Positive Predictive Value	0.748
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...	0.75	0.57	1.00	17	2833	1	0	0	1	13
3J2L_3	5S_rRNA links to Rfam database...	0.45	0.32	0.63	17	7848	11	1	9	1	36
3J3D_C	tRNA links to Rfam database...	0.76	0.61	0.94	17	2757	1	0	1	0	11
3J3E_8	5_8S_rRNA links to Rfam database...	0.10	0.06	0.17	2	7491	10	1	9	0	31
3J3E_7	5S_rRNA links to Rfam database...	0.62	0.46	0.83	25	7110	5	1	4	0	29
3J3F_8	5_8S_rRNA links to Rfam database...	0.45	0.33	0.60	12	12226	8	1	7	0	24
3J3F_7	5S_rRNA links to Rfam database...	0.66	0.52	0.84	26	7229	6	0	5	1	24
3J3V_B	5S_rRNA links to Rfam database...	0.38	0.21	0.71	12	7004	5	0	5	0	45
3ZEX_D	5S_rRNA links to Rfam database...	0.58	0.39	0.86	19	6999	3	0	3	0	30
3ZND_W	tRNA links to Rfam database...	0.45	0.39	0.53	9	2986	11	0	8	3	14
4FRG_B	AdoCbl-variant links to Rfam database...	0.47	0.22	1.00	7	3479	0	0	0	0	25

Total Scores
MCC	0.446
Average MCC ± 95% Confidence Intervals	0.430 ± 0.140
Sensitivity	0.393
Positive Predictive Value	0.513
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...	0.43	0.40	0.48	12	2825	14	0	13	1	18
3J2L_3	5S_rRNA links to Rfam database...	0.59	0.51	0.69	27	7836	14	0	12	2	26
3J3D_C	tRNA links to Rfam database...	0.60	0.54	0.68	15	2753	7	0	7	0	13
3J3E_8	5_8S_rRNA links to Rfam database...	0.17	0.15	0.19	5	7477	29	2	19	8	28
3J3E_7	5S_rRNA links to Rfam database...	0.48	0.41	0.58	22	7102	16	1	15	0	32
3J3F_8	5_8S_rRNA links to Rfam database...	0.30	0.31	0.30	11	12209	39	3	23	13	25
3J3F_7	5S_rRNA links to Rfam database...	0.68	0.58	0.81	29	7224	7	1	6	0	21
3J3V_B	5S_rRNA links to Rfam database...	0.20	0.16	0.26	9	6987	25	0	25	0	48
3ZEX_D	5S_rRNA links to Rfam database...	0.76	0.63	0.91	31	6987	3	0	3	0	18
3ZND_W	tRNA links to Rfam database...	0.20	0.22	0.19	5	2977	22	1	20	1	18
4FRG_B	AdoCbl-variant links to Rfam database...	0.32	0.28	0.38	9	3462	15	0	15	0	23

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