CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	PPfold(20)		RNAshapes
MCC	0.668	>	0.491
Average MCC ± 95% Confidence Intervals	0.643 ± 0.170	>	0.507 ± 0.155
Sensitivity	0.614	>	0.529
Positive Predictive Value	0.733	>	0.466
Total TP	159	>	137
Total TN	25369	>	25292
Total FP	79	<	218
Total FP CONTRA	14	<	49
Total FP INCONS	44	<	108
Total FP COMP	21	<	61
Total FN	100	<	122
P-value	2.00627773251e-08

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

Total Scores
MCC	0.668
Average MCC ± 95% Confidence Intervals	0.643 ± 0.170
Sensitivity	0.614
Positive Predictive Value	0.733
Nr of predictions	12

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	1	1	0	0	1
3J3D_C	tRNA links to Rfam database...	0.87	0.89	0.85	17	948	3	3	0	0	2
3J3E_8	5_8S_rRNA links to Rfam database...	0.21	0.20	0.23	3	2729	13	2	8	3	12
3J3F_8	5_8S_rRNA links to Rfam database...	0.37	0.37	0.37	7	4742	20	5	7	8	12
3RKF_A	Purine links to Rfam database...	0.86	0.79	0.95	19	846	1	0	1	0	5
3SD1_A	THF links to Rfam database...	0.81	0.76	0.88	22	1508	3	2	1	0	7
3ZEX_C	5_8S_rRNA links to Rfam database...	0.38	0.31	0.47	9	5355	14	0	10	4	20
4A1C_2	5_8S_rRNA links to Rfam database...	0.27	0.25	0.29	5	4499	16	1	11	4	15
4AOB_A	SAM links to Rfam database...	0.87	0.83	0.92	24	1411	4	0	2	2	5
4ENB_A	crcB links to Rfam database...	0.63	0.47	0.88	7	464	1	0	1	0	8
4ENC_A	crcB links to Rfam database...	0.64	0.53	0.80	8	486	2	0	2	0	7
4FRG_B	AdoCbl-variant links to Rfam database...	0.84	0.75	0.95	18	1183	1	0	1	0	6

Total Scores
MCC	0.491
Average MCC ± 95% Confidence Intervals	0.507 ± 0.155
Sensitivity	0.529
Positive Predictive Value	0.466
Nr of predictions	12

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
3J20_0	tRNA links to Rfam database...	0.51	0.57	0.48	12	1194	14	3	10	1	9
3J3D_C	tRNA links to Rfam database...	0.63	0.68	0.59	13	946	9	3	6	0	6
3J3E_8	5_8S_rRNA links to Rfam database...	0.26	0.33	0.21	5	2718	29	6	13	10	10
3J3F_8	5_8S_rRNA links to Rfam database...	0.33	0.42	0.26	8	4730	42	11	12	19	11
3RKF_A	Purine links to Rfam database...	0.91	0.83	1.00	20	846	0	0	0	0	4
3SD1_A	THF links to Rfam database...	0.77	0.76	0.79	22	1505	6	4	2	0	7
3ZEX_C	5_8S_rRNA links to Rfam database...	0.29	0.34	0.26	10	5335	42	5	24	13	19
4A1C_2	5_8S_rRNA links to Rfam database...	0.19	0.25	0.16	5	4484	41	11	16	14	15
4AOB_A	SAM links to Rfam database...	0.60	0.59	0.63	17	1410	11	4	6	1	12
4ENB_A	crcB links to Rfam database...	0.85	0.73	1.00	11	461	2	0	0	2	4
4ENC_A	crcB links to Rfam database...	0.37	0.33	0.45	5	485	7	0	6	1	10
4FRG_B	AdoCbl-variant links to Rfam database...	0.36	0.38	0.38	9	1178	15	2	13	0	15

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