CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	RNASLOpt		Murlet(seed)
MCC	0.426	>	0.400
Average MCC ± 95% Confidence Intervals	0.469 ± 0.185	>	0.405 ± 0.161
Sensitivity	0.352	>	0.225
Positive Predictive Value	0.523	<	0.717
Total TP	103	>	66
Total TN	47682	<	47787
Total FP	114	>	27
Total FP CONTRA	16	>	1
Total FP INCONS	78	>	25
Total FP COMP	20	>	1
Total FN	190	<	227
P-value	0.0

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

Total Scores
MCC	0.426
Average MCC ± 95% Confidence Intervals	0.469 ± 0.185
Sensitivity	0.352
Positive Predictive Value	0.523
Nr of predictions	9

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...	0.47	0.35	0.64	7	1529	4	0	4	0	13
3W3S_B	tRNA-Sec links to Rfam database...	0.82	0.70	0.97	28	4724	2	0	1	1	12
3ZEX_C	5_8S_rRNA links to Rfam database...	0.26	0.21	0.33	11	14163	35	2	20	13	41
4A1C_2	5_8S_rRNA links to Rfam database...	0.23	0.24	0.22	8	11744	35	8	21	6	25
4AOB_A	SAM links to Rfam database...	0.26	0.19	0.38	8	4350	13	2	11	0	34
4ENB_A	crcB links to Rfam database...	0.76	0.58	1.00	11	1264	0	0	0	0	8
4ENC_A	crcB links to Rfam database...	0.65	0.47	0.90	9	1316	1	1	0	0	10
4FRG_B	AdoCbl-variant links to Rfam database...	0.56	0.47	0.68	15	3464	7	1	6	0	17
4FRN_A	AdoCbl-variant links to Rfam database...	0.20	0.17	0.26	6	5128	17	2	15	0	30

Total Scores
MCC	0.400
Average MCC ± 95% Confidence Intervals	0.405 ± 0.161
Sensitivity	0.225
Positive Predictive Value	0.717
Nr of predictions	9

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...	-0.01	0.00	0.00	0	1528	12	0	12	0	20
3W3S_B	tRNA-Sec links to Rfam database...	0.41	0.23	0.75	9	4741	3	0	3	0	31
3ZEX_C	5_8S_rRNA links to Rfam database...	0.37	0.13	1.00	7	14189	0	0	0	0	45
4A1C_2	5_8S_rRNA links to Rfam database...	0.46	0.21	1.00	7	11774	0	0	0	0	26
4AOB_A	SAM links to Rfam database...	0.58	0.33	1.00	14	4357	1	0	0	1	28
4ENB_A	crcB links to Rfam database...	0.56	0.32	1.00	6	1269	0	0	0	0	13
4ENC_A	crcB links to Rfam database...	0.56	0.32	1.00	6	1320	0	0	0	0	13
4FRG_B	AdoCbl-variant links to Rfam database...	0.15	0.09	0.25	3	3474	9	0	9	0	29
4FRN_A	AdoCbl-variant links to Rfam database...	0.58	0.39	0.88	14	5135	2	1	1	0	22

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