CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	PPfold(20)		Vsfold5
MCC	0.844	>	0.546
Average MCC ± 95% Confidence Intervals	0.812 ± 0.116	>	0.604 ± 0.189
Sensitivity	0.791	>	0.544
Positive Predictive Value	0.906	>	0.561
Total TP	269	>	185
Total TN	22649	>	22616
Total FP	45	<	175
Total FP CONTRA	4	<	37
Total FP INCONS	24	<	108
Total FP COMP	17	<	30
Total FN	71	<	155
P-value	2.1413769576e-08

Comparison of performance of PPfold(20) and Vsfold5. 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 Vsfold5).
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 Vsfold5).
Comparison of average Matthews Correlation Coefficients (MCCs) for PPfold(20) and Vsfold5. 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 Vsfold5).

Total Scores
MCC	0.844
Average MCC ± 95% Confidence Intervals	0.812 ± 0.116
Sensitivity	0.791
Positive Predictive Value	0.906
Nr of predictions	14

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2L94_A	HIV_FE links to Rfam database...	0.66	0.50	0.90	9	347	1	0	1	0	9
3AMU_B	tRNA links to Rfam database...	1.00	1.00	1.00	19	1138	2	0	0	2	0
3J20_1	tRNA links to Rfam database...	1.00	1.00	1.00	20	1092	1	0	0	1	0
3J20_0	tRNA links to Rfam database...	0.95	0.95	0.95	20	1198	1	1	0	0	1
3J2L_3	5S_rRNA links to Rfam database...	0.97	0.94	1.00	32	2988	4	0	0	4	2
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_D	5S_rRNA links to Rfam database...	0.93	0.91	0.94	32	2762	6	0	2	4	3
4A1C_3	5S_rRNA links to Rfam database...	0.93	0.92	0.94	34	2727	2	0	2	0	3
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	0.546
Average MCC ± 95% Confidence Intervals	0.604 ± 0.189
Sensitivity	0.544
Positive Predictive Value	0.561
Nr of predictions	14

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2L94_A	HIV_FE links to Rfam database...	0.97	0.94	1.00	17	340	1	0	0	1	1
3AMU_B	tRNA links to Rfam database...	0.77	0.79	0.75	15	1137	8	0	5	3	4
3J20_1	tRNA links to Rfam database...	0.75	0.75	0.75	15	1092	7	0	5	2	5
3J20_0	tRNA links to Rfam database...	0.76	0.76	0.76	16	1198	6	3	2	1	5
3J2L_3	5S_rRNA links to Rfam database...	0.70	0.71	0.71	24	2986	13	3	7	3	10
3RKF_A	Purine links to Rfam database...	0.90	0.92	0.88	22	841	3	3	0	0	2
3SD1_A	THF links to Rfam database...	0.13	0.14	0.15	4	1507	22	5	17	0	25
3ZEX_D	5S_rRNA links to Rfam database...	0.09	0.09	0.12	3	2771	24	5	17	2	32
4A1C_3	5S_rRNA links to Rfam database...	0.29	0.30	0.31	11	2727	26	4	21	1	26
4A1C_2	5_8S_rRNA links to Rfam database...	0.33	0.40	0.28	8	4487	37	8	13	16	12
4AOB_A	SAM links to Rfam database...	0.21	0.21	0.25	6	1413	19	2	16	1	23
4ENB_A	crcB links to Rfam database...	1.00	1.00	1.00	15	457	0	0	0	0	0
4ENC_A	crcB links to Rfam database...	0.97	1.00	0.94	15	480	1	1	0	0	0
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.