CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	Vsfold4		Multilign(20)
MCC	0.526	>	0.517
Average MCC ± 95% Confidence Intervals	0.555 ± 0.192	>	0.513 ± 0.207
Sensitivity	0.535	>	0.530
Positive Predictive Value	0.528	>	0.515
Total TP	123	>	122
Total TN	19979	>	19975
Total FP	147	>	139
Total FP CONTRA	40	>	39
Total FP INCONS	70	<	76
Total FP COMP	37	>	24
Total FN	107	<	108
P-value	0.00216473880436

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

Total Scores
MCC	0.526
Average MCC ± 95% Confidence Intervals	0.555 ± 0.192
Sensitivity	0.535
Positive Predictive Value	0.528
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...	0.95	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
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...	0.23	0.24	0.24	7	1504	22	5	17	0	22
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

Total Scores
MCC	0.517
Average MCC ± 95% Confidence Intervals	0.513 ± 0.207
Sensitivity	0.530
Positive Predictive Value	0.515
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...	0.68	0.71	0.65	15	1196	9	2	6	1	6
3J3D_C	tRNA links to Rfam database...	0.90	0.95	0.86	18	947	3	3	0	0	1
3J3E_8	5_8S_rRNA links to Rfam database...	-0.01	0.00	0.00	0	2720	22	8	14	0	15
3J3F_8	5_8S_rRNA links to Rfam database...	0.45	0.53	0.38	10	4735	30	7	9	14	9
3RKF_A	Purine links to Rfam database...	0.91	0.88	0.95	21	844	1	0	1	0	3
3SD1_A	THF links to Rfam database...	0.68	0.69	0.69	20	1504	9	4	5	0	9
4A1C_2	5_8S_rRNA links to Rfam database...	0.20	0.25	0.16	5	4485	33	9	17	7	15
4AOB_A	SAM links to Rfam database...	0.59	0.55	0.64	16	1412	10	3	6	1	13
4ENB_A	crcB links to Rfam database...	0.39	0.33	0.50	5	462	6	0	5	1	10
4ENC_A	crcB links to Rfam database...	0.73	0.60	0.90	9	486	1	1	0	0	6
4FRG_B	AdoCbl-variant links to Rfam database...	0.13	0.13	0.17	3	1184	15	2	13	0	21

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