CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	PPfold(20)		Murlet(seed)
MCC	0.681	>	0.543
Average MCC ± 95% Confidence Intervals	0.664 ± 0.166	>	0.550 ± 0.119
Sensitivity	0.596	>	0.360
Positive Predictive Value	0.786	<	0.830
Total TP	121	>	73
Total TN	16099	<	16165
Total FP	43	>	17
Total FP CONTRA	3	>	1
Total FP INCONS	30	>	14
Total FP COMP	10	>	2
Total FN	82	<	130
P-value	0.0

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

Total Scores
MCC	0.681
Average MCC ± 95% Confidence Intervals	0.664 ± 0.166
Sensitivity	0.596
Positive Predictive Value	0.786
Nr of predictions	9

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
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_C	5_8S_rRNA links to Rfam database...	0.38	0.31	0.47	9	5355	14	0	10	4	20
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	0.543
Average MCC ± 95% Confidence Intervals	0.550 ± 0.119
Sensitivity	0.360
Positive Predictive Value	0.830
Nr of predictions	9

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...	0.57	0.39	0.88	7	349	2	0	1	1	11
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
3ZEX_C	5_8S_rRNA links to Rfam database...	0.49	0.24	1.00	7	5367	0	0	0	0	22
4A1C_2	5_8S_rRNA links to Rfam database...	0.59	0.35	1.00	7	4509	0	0	0	0	13
4AOB_A	SAM links to Rfam database...	0.69	0.48	1.00	14	1423	1	0	0	1	15
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
4FRG_B	AdoCbl-variant links to Rfam database...	0.17	0.13	0.25	3	1190	9	0	9	0	21

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