CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	RNAalifold(20)		Cylofold
MCC	0.787	>	0.703
Average MCC ± 95% Confidence Intervals	0.741 ± 0.122	>	0.728 ± 0.162
Sensitivity	0.689	<	0.703
Positive Predictive Value	0.904	>	0.711
Total TP	244	<	249
Total TN	26055	>	25975
Total FP	47	<	136
Total FP CONTRA	8	<	31
Total FP INCONS	18	<	70
Total FP COMP	21	<	35
Total FN	110	>	105
P-value	2.10198558684e-08

Comparison of performance of RNAalifold(20) and Cylofold. 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 RNAalifold(20) and Cylofold).
Comparison of average Matthews Correlation Coefficients (MCCs) for RNAalifold(20) and Cylofold. 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 RNAalifold(20) and Cylofold).

Total Scores
MCC	0.787
Average MCC ± 95% Confidence Intervals	0.741 ± 0.122
Sensitivity	0.689
Positive Predictive Value	0.904
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...	0.51	0.50	0.56	9	341	8	0	7	1	9
2XKV_B	Bacteria_small_SRP links to Rfam database...	0.60	0.36	1.00	4	1831	3	0	0	3	7
2XQD_Y	tRNA links to Rfam database...	0.98	0.95	1.00	20	1109	1	0	0	1	1
2XXA_G	Bacteria_small_SRP links to Rfam database...	0.44	0.20	1.00	7	2038	0	0	0	0	28
3AMU_B	tRNA links to Rfam database...	1.00	1.00	1.00	19	1138	2	0	0	2	0
3IZF_C	5S_rRNA links to Rfam database...	0.90	0.89	0.91	31	2606	6	0	3	3	4
3O58_2	5S_rRNA links to Rfam database...	0.97	0.94	1.00	29	2725	7	0	0	7	2
3O58_3	5_8S_rRNA links to Rfam database...	0.42	0.36	0.50	8	4748	9	3	5	1	14
3PDR_A	ykoK links to Rfam database...	0.92	0.88	0.96	44	4794	3	1	1	1	6
3RKF_A	Purine links to Rfam database...	0.81	0.71	0.94	17	848	1	0	1	0	7
3SD1_A	THF links to Rfam database...	0.84	0.86	0.83	25	1503	5	4	1	0	4
4AOB_A	SAM links to Rfam database...	0.85	0.72	1.00	21	1416	2	0	0	2	8
4ENB_A	crcB links to Rfam database...	0.51	0.27	1.00	4	468	0	0	0	0	11
4ENC_A	crcB links to Rfam database...	0.63	0.40	1.00	6	490	0	0	0	0	9

Total Scores
MCC	0.703
Average MCC ± 95% Confidence Intervals	0.728 ± 0.162
Sensitivity	0.703
Positive Predictive Value	0.711
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...	1.00	1.00	1.00	18	339	1	0	0	1	0
2XKV_B	Bacteria_small_SRP links to Rfam database...	0.41	0.55	0.32	6	1816	25	9	4	12	5
2XQD_Y	tRNA links to Rfam database...	0.89	0.95	0.83	20	1105	5	4	0	1	1
2XXA_G	Bacteria_small_SRP links to Rfam database...	0.10	0.11	0.11	4	2009	32	2	30	0	31
3AMU_B	tRNA links to Rfam database...	0.77	0.79	0.75	15	1137	8	0	5	3	4
3IZF_C	5S_rRNA links to Rfam database...	0.85	0.83	0.88	29	2607	7	0	4	3	6
3O58_2	5S_rRNA links to Rfam database...	0.90	0.84	0.96	26	2727	3	0	1	2	5
3O58_3	5_8S_rRNA links to Rfam database...	0.42	0.50	0.35	11	4733	30	9	11	10	11
3PDR_A	ykoK links to Rfam database...	0.86	0.78	0.95	39	4799	4	1	1	2	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...	0.71	0.69	0.74	20	1506	7	2	5	0	9
4AOB_A	SAM links to Rfam database...	0.42	0.38	0.48	11	1414	13	3	9	1	18
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

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