CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	MCFold		Murlet(seed)
MCC	0.567	>	0.558
Average MCC ± 95% Confidence Intervals	0.548 ± 0.162	<	0.556 ± 0.122
Sensitivity	0.599	>	0.381
Positive Predictive Value	0.547	<	0.826
Total TP	179	>	114
Total TN	22494	<	22683
Total FP	184	>	26
Total FP CONTRA	40	>	4
Total FP INCONS	108	>	20
Total FP COMP	36	>	2
Total FN	120	<	185
P-value	0.206948167051

Comparison of performance of MCFold and Murlet(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 MCFold and Murlet(seed)).
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 MCFold and Murlet(seed)).
Comparison of average Matthews Correlation Coefficients (MCCs) for MCFold and Murlet(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 MCFold and Murlet(seed)).

Total Scores
MCC	0.567
Average MCC ± 95% Confidence Intervals	0.548 ± 0.162
Sensitivity	0.599
Positive Predictive Value	0.547
Nr of predictions	12

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...	0.44	0.44	0.47	8	511	10	0	9	1	10
3A3A_A	tRNA-Sec links to Rfam database...	0.98	0.97	1.00	29	1471	0	0	0	0	1
3GX2_A	SAM links to Rfam database...	0.58	0.61	0.57	17	1419	15	1	12	2	11
3IVN_B	Purine links to Rfam database...	0.45	0.48	0.46	11	879	14	5	8	1	12
3LA5_A	Purine links to Rfam database...	0.44	0.44	0.48	11	931	12	2	10	0	14
3O58_3	5_8S_rRNA links to Rfam database...	0.28	0.36	0.22	8	4727	39	14	15	10	14
3PDR_A	ykoK links to Rfam database...	0.78	0.80	0.77	40	4788	14	5	7	2	10
3RKF_A	Purine links to Rfam database...	0.89	0.88	0.91	21	843	3	0	2	1	3
3SD1_A	THF links to Rfam database...	0.43	0.45	0.43	13	1503	17	1	16	0	16
4A1C_2	5_8S_rRNA links to Rfam database...	0.18	0.25	0.14	5	4480	45	12	19	14	15
4ENB_A	crcB links to Rfam database...	0.78	0.73	0.85	11	459	4	0	2	2	4
4ENC_A	crcB links to Rfam database...	0.34	0.33	0.38	5	483	11	0	8	3	10

Total Scores
MCC	0.558
Average MCC ± 95% Confidence Intervals	0.556 ± 0.122
Sensitivity	0.381
Positive Predictive Value	0.826
Nr of predictions	12

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	0	12	0	18
3A3A_A	tRNA-Sec links to Rfam database...	0.63	0.40	1.00	12	1488	0	0	0	0	18
3GX2_A	SAM links to Rfam database...	0.70	0.50	1.00	14	1435	1	0	0	1	14
3IVN_B	Purine links to Rfam database...	0.62	0.52	0.75	12	887	4	2	2	0	11
3LA5_A	Purine links to Rfam database...	0.67	0.56	0.82	14	937	3	1	2	0	11
3O58_3	5_8S_rRNA links to Rfam database...	0.52	0.27	1.00	6	4758	1	0	0	1	16
3PDR_A	ykoK links to Rfam database...	0.53	0.28	1.00	14	4826	0	0	0	0	36
3RKF_A	Purine links to Rfam database...	0.62	0.50	0.80	12	851	3	1	2	0	12
3SD1_A	THF links to Rfam database...	0.56	0.38	0.85	11	1520	2	0	2	0	18
4A1C_2	5_8S_rRNA links to Rfam database...	0.59	0.35	1.00	7	4509	0	0	0	0	13
4ENB_A	crcB links to Rfam database...	0.63	0.40	1.00	6	466	0	0	0	0	9
4ENC_A	crcB links to Rfam database...	0.63	0.40	1.00	6	490	0	0	0	0	9

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