CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	PETfold_pre2.0(20)		Vsfold4
MCC	0.678	>	0.527
Average MCC ± 95% Confidence Intervals	0.660 ± 0.199	>	0.552 ± 0.208
Sensitivity	0.655	>	0.542
Positive Predictive Value	0.707	>	0.522
Total TP	116	>	96
Total TN	17649	>	17629
Total FP	74	<	125
Total FP CONTRA	13	<	35
Total FP INCONS	35	<	53
Total FP COMP	26	<	37
Total FN	61	<	81
P-value	0.0

Comparison of performance of PETfold_pre2.0(20) and Vsfold4. 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 PETfold_pre2.0(20) and Vsfold4).
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 PETfold_pre2.0(20) and Vsfold4).
Comparison of average Matthews Correlation Coefficients (MCCs) for PETfold_pre2.0(20) and Vsfold4. 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 PETfold_pre2.0(20) and Vsfold4).

Total Scores
MCC	0.678
Average MCC ± 95% Confidence Intervals	0.660 ± 0.199
Sensitivity	0.655
Positive Predictive Value	0.707
Nr of predictions	9

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...	0.48	0.47	0.50	7	2728	11	2	5	4	8
3J3F_8	5_8S_rRNA links to Rfam database...	0.34	0.37	0.32	7	4739	24	5	10	9	12
4A1C_2	5_8S_rRNA links to Rfam database...	0.25	0.25	0.25	5	4496	25	2	13	10	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...	0.68	0.53	0.89	8	463	1	0	1	0	7
4ENC_A	crcB links to Rfam database...	0.61	0.53	0.73	8	485	3	0	3	0	7
4FRG_B	AdoCbl-variant links to Rfam database...	0.89	0.83	0.95	20	1181	2	0	1	1	4

Total Scores
MCC	0.527
Average MCC ± 95% Confidence Intervals	0.552 ± 0.208
Sensitivity	0.542
Positive Predictive Value	0.522
Nr of predictions	9

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
3J3D_C	tRNA links to Rfam database...	0.48	0.53	0.45	10	946	12	4	8	0	9
3J3E_8	5_8S_rRNA links to Rfam database...	0.10	0.13	0.09	2	2720	32	9	11	12	13
3J3F_8	5_8S_rRNA links to Rfam database...	0.35	0.42	0.30	8	4734	30	11	8	11	11
4A1C_2	5_8S_rRNA links to Rfam database...	0.36	0.40	0.33	8	4492	28	4	12	12	12
4AOB_A	SAM links to Rfam database...	0.50	0.48	0.54	14	1411	13	3	9	1	15
4ENB_A	crcB links to Rfam database...	0.85	0.73	1.00	11	461	0	0	0	0	4
4ENC_A	crcB links to Rfam database...	0.77	0.60	1.00	9	487	0	0	0	0	6
4FRG_B	AdoCbl-variant links to Rfam database...	0.60	0.58	0.64	14	1180	8	3	5	0	10

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