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

Home

RNA 2D Atlas

Help

FAQ

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 RNAsubopt - scored lower in this pairwise comparison

Total counts & total scores
Individual counts

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

Overview

Metric	PETfold_pre2.0(20)		RNAsubopt
MCC	0.625	>	0.477
Average MCC ± 95% Confidence Intervals	0.581 ± 0.300	>	0.475 ± 0.302
Sensitivity	0.497	>	0.425
Positive Predictive Value	0.790	>	0.542
Total TP	83	>	71
Total TN	25788	>	25762
Total FP	33	<	70
Total FP CONTRA	0	<	9
Total FP INCONS	22	<	51
Total FP COMP	11	>	10
Total FN	84	<	96
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 RNAsubopt - scored lower in this pairwise comparison

1. Total counts & total scores for RNAsubopt

Total Base Pair Counts
Total TP	71
Total TN	25762
Total FP	70
Total FP CONTRA	9
Total FP INCONS	51
Total FP COMP	10
Total FN	96

Total Scores
MCC	0.477
Average MCC ± 95% Confidence Intervals	0.475 ± 0.302
Sensitivity	0.425
Positive Predictive Value	0.542
Nr of predictions	5

2. Individual counts for RNAsubopt [ 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...	0.14	0.15	0.13	5	11742	43	5	29	9	28
4A1C_3	5S_rRNA links to Rfam database...	0.70	0.59	0.82	32	7101	7	1	6	0	22
4AOB_A	SAM links to Rfam database...	0.52	0.43	0.64	18	4343	11	2	8	1	24
4ENB_A	crcB links to Rfam database...	0.70	0.58	0.85	11	1262	2	1	1	0	8
4ENC_A	crcB links to Rfam database...	0.32	0.26	0.42	5	1314	7	0	7	0	14

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