CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	PETfold_pre2.0(seed)		Multilign(seed)
MCC	0.766	>	0.628
Average MCC ± 95% Confidence Intervals	0.740 ± 0.121	>	0.554 ± 0.317
Sensitivity	0.686	>	0.575
Positive Predictive Value	0.861	>	0.696
Total TP	142	>	119
Total TN	16513	>	16507
Total FP	43	<	55
Total FP CONTRA	8	<	17
Total FP INCONS	15	<	35
Total FP COMP	20	>	3
Total FN	65	<	88
P-value	0.0

Comparison of performance of PETfold_pre2.0(seed) and Multilign(seed). 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(seed) and Multilign(seed)).
Comparison of performance of PETfold_pre2.0(seed) and Multilign(seed). 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(seed) and Multilign(seed)).
Comparison of average Matthews Correlation Coefficients (MCCs) for PETfold_pre2.0(seed) and Multilign(seed). 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(seed) and Multilign(seed)).
Comparison of average Matthews Correlation Coefficients (MCCs) for PETfold_pre2.0(seed) and Multilign(seed). 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(seed) and Multilign(seed)).

Total Scores
MCC	0.766
Average MCC ± 95% Confidence Intervals	0.740 ± 0.121
Sensitivity	0.686
Positive Predictive Value	0.861
Nr of predictions	8

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2LC8_A	GP_knot1 links to Rfam database...	0.41	0.33	0.55	6	517	5	0	5	0	12
3J3E_8	5_8S_rRNA links to Rfam database...	0.71	0.67	0.77	10	2729	8	1	2	5	5
3W1K_J	tRNA-Sec links to Rfam database...	0.85	0.81	0.89	25	1650	4	2	1	1	6
3W3S_B	tRNA-Sec links to Rfam database...	0.80	0.73	0.89	24	1962	6	1	2	3	9
3ZEX_C	5_8S_rRNA links to Rfam database...	0.70	0.59	0.85	17	5354	12	1	2	9	12
4AOB_A	SAM links to Rfam database...	0.85	0.79	0.92	23	1412	4	0	2	2	6
4FRN_A	AdoCbl-variant links to Rfam database...	0.83	0.79	0.88	22	1823	3	2	1	0	6
4JF2_A	preQ1-II links to Rfam database...	0.76	0.63	0.94	15	1066	1	1	0	0	9

Total Scores
MCC	0.628
Average MCC ± 95% Confidence Intervals	0.554 ± 0.317
Sensitivity	0.575
Positive Predictive Value	0.696
Nr of predictions	8

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2LC8_A	GP_knot1 links to Rfam database...	-0.03	0.00	0.00	0	516	12	2	10	0	18
3J3E_8	5_8S_rRNA links to Rfam database...	0.19	0.20	0.19	3	2726	13	8	5	0	12
3W1K_J	tRNA-Sec links to Rfam database...	0.97	0.97	0.97	30	1647	1	1	0	0	1
3W3S_B	tRNA-Sec links to Rfam database...	0.92	0.88	0.97	29	1959	2	0	1	1	4
3ZEX_C	5_8S_rRNA links to Rfam database...	0.50	0.45	0.57	13	5351	11	3	7	1	16
4AOB_A	SAM links to Rfam database...	0.73	0.66	0.83	19	1414	5	1	3	1	10
4FRN_A	AdoCbl-variant links to Rfam database...	0.27	0.21	0.35	6	1831	11	2	9	0	22
4JF2_A	preQ1-II links to Rfam database...	0.89	0.79	1.00	19	1063	0	0	0	0	5

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