CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	PPfold(20)		CentroidAlifold(20)
MCC	0.746	>	0.745
Average MCC ± 95% Confidence Intervals	0.747 ± 0.127	>	0.739 ± 0.157
Sensitivity	0.681	>	0.631
Positive Predictive Value	0.818	<	0.880
Total TP	1989	>	1842
Total TN	7954946	<	7955283
Total FP	607	>	384
Total FP CONTRA	71	>	47
Total FP INCONS	371	>	205
Total FP COMP	165	>	132
Total FN	931	<	1078
P-value	0.0

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

Total Scores
MCC	0.746
Average MCC ± 95% Confidence Intervals	0.747 ± 0.127
Sensitivity	0.681
Positive Predictive Value	0.818
Nr of predictions	6

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
CRW_00256	SSU_rRNA_bacteria links to Rfam database...	0.82	0.78	0.87	363	1192324	70	13	40	17	105
CRW_00326	SSU_rRNA_eukarya links to Rfam database...	0.64	0.56	0.73	280	1627728	143	17	85	41	222
CRW_00358	SSU_rRNA_eukarya links to Rfam database...	0.56	0.49	0.64	246	1674980	178	15	124	39	261
CRW_00590	SSU_rRNA_bacteria links to Rfam database...	0.85	0.81	0.90	367	1119348	69	4	37	28	85
CRW_00997	SSU_rRNA_bacteria links to Rfam database...	0.83	0.81	0.86	374	1135845	75	15	44	16	90
PDB_01120	SSU_rRNA_bacteria links to Rfam database...	0.78	0.68	0.88	359	1204721	72	7	41	24	168

Total Scores
MCC	0.745
Average MCC ± 95% Confidence Intervals	0.739 ± 0.157
Sensitivity	0.631
Positive Predictive Value	0.880
Nr of predictions	6

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
CRW_00256	SSU_rRNA_bacteria links to Rfam database...	0.84	0.77	0.91	360	1192345	51	10	25	16	108
CRW_00326	SSU_rRNA_eukarya links to Rfam database...	0.57	0.40	0.80	201	1627859	78	6	44	28	301
CRW_00358	SSU_rRNA_eukarya links to Rfam database...	0.53	0.39	0.73	196	1675098	99	8	63	28	311
CRW_00590	SSU_rRNA_bacteria links to Rfam database...	0.86	0.79	0.93	359	1119369	53	3	25	25	93
CRW_00997	SSU_rRNA_bacteria links to Rfam database...	0.85	0.80	0.91	369	1135873	50	13	23	14	95
PDB_01120	SSU_rRNA_bacteria links to Rfam database...	0.79	0.68	0.92	357	1204739	53	7	25	21	170

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