CompaRNA - on-line benchmarks of RNA structure prediction methods

CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

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Table of contents:

Overview

Performance Plots

Performance of PETfold_pre2.0(20) - scored higher in this pairwise comparison

Total counts & total scores
Individual counts

Performance of IPknot - scored lower in this pairwise comparison

Total counts & total scores
Individual counts

Compile and download dataset for PETfold_pre2.0(20) & IPknot [.zip] - may take several seconds...

Overview

Metric	PETfold_pre2.0(20)		IPknot
MCC	0.625	>	0.502
Average MCC ± 95% Confidence Intervals	0.581 ± 0.300	>	0.513 ± 0.291
Sensitivity	0.497	>	0.413
Positive Predictive Value	0.790	>	0.616
Total TP	83	>	69
Total TN	25788	>	25781
Total FP	33	<	49
Total FP CONTRA	0	<	6
Total FP INCONS	22	<	37
Total FP COMP	11	>	6
Total FN	84	<	98
P-value	0.0

Performance plots

Performance of PETfold_pre2.0(20) - scored higher in this pairwise comparison

1. Total counts & total scores for PETfold_pre2.0(20)

Total Base Pair Counts
Total TP	83
Total TN	25788
Total FP	33
Total FP CONTRA	0
Total FP INCONS	22
Total FP COMP	11
Total FN	84

Total Scores
MCC	0.625
Average MCC ± 95% Confidence Intervals	0.581 ± 0.300
Sensitivity	0.497
Positive Predictive Value	0.790
Nr of predictions	5

2. Individual counts for PETfold_pre2.0(20) [ download as .csv ]

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
4A1C_2	5_8S_rRNA links to Rfam database...	0.19	0.15	0.25	5	11761	25	0	15	10	28
4A1C_3	5S_rRNA links to Rfam database...	0.82	0.69	0.97	37	7102	1	0	1	0	17
4AOB_A	SAM links to Rfam database...	0.74	0.60	0.93	25	4344	3	0	2	1	17
4ENB_A	crcB links to Rfam database...	0.61	0.42	0.89	8	1266	1	0	1	0	11
4ENC_A	crcB links to Rfam database...	0.55	0.42	0.73	8	1315	3	0	3	0	11

Performance of IPknot - scored lower in this pairwise comparison

1. Total counts & total scores for IPknot

Total Base Pair Counts
Total TP	69
Total TN	25781
Total FP	49
Total FP CONTRA	6
Total FP INCONS	37
Total FP COMP	6
Total FN	98

Total Scores
MCC	0.502
Average MCC ± 95% Confidence Intervals	0.513 ± 0.291
Sensitivity	0.413
Positive Predictive Value	0.616
Nr of predictions	5

2. Individual counts for IPknot [ download as .csv ]

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
4A1C_2	5_8S_rRNA links to Rfam database...	0.17	0.15	0.19	5	11755	26	4	17	5	28
4A1C_3	5S_rRNA links to Rfam database...	0.69	0.57	0.84	31	7103	6	1	5	0	23
4AOB_A	SAM links to Rfam database...	0.42	0.33	0.54	14	4345	13	1	11	1	28
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...	0.52	0.42	0.67	8	1314	4	0	4	0	11

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