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 RNASampler(20) - scored higher in this pairwise comparison

Total counts & total scores
Individual counts

Performance of PPfold(seed) - scored lower in this pairwise comparison

Total counts & total scores
Individual counts

Compile and download dataset for RNASampler(20) & PPfold(seed) [.zip] - may take several seconds...

Overview

Metric	RNASampler(20)		PPfold(seed)
MCC	0.637	>	0.026
Average MCC ± 95% Confidence Intervals	0.641 ± 0.169	>	0.010 ± 0.023
Sensitivity	0.478	>	0.004
Positive Predictive Value	0.854	>	0.200
Total TP	129	>	1
Total TN	34872	<	35018
Total FP	38	>	23
Total FP CONTRA	0	=	0
Total FP INCONS	22	>	4
Total FP COMP	16	<	19
Total FN	141	<	269
P-value	0.0

Performance plots

Performance of RNASampler(20) - scored higher in this pairwise comparison

1. Total counts & total scores for RNASampler(20)

Total Base Pair Counts
Total TP	129
Total TN	34872
Total FP	38
Total FP CONTRA	0
Total FP INCONS	22
Total FP COMP	16
Total FN	141

Total Scores
MCC	0.637
Average MCC ± 95% Confidence Intervals	0.641 ± 0.169
Sensitivity	0.478
Positive Predictive Value	0.854
Nr of predictions	8

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

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
3AMU_B	tRNA links to Rfam database...	0.82	0.70	0.95	19	2983	3	0	1	2	8
3RKF_A	Purine links to Rfam database...	0.76	0.59	1.00	20	2191	0	0	0	0	14
3SD1_A	THF links to Rfam database...	0.67	0.48	0.95	20	3895	1	0	1	0	22
4A1C_2	5_8S_rRNA links to Rfam database...	0.18	0.15	0.23	5	11759	30	0	17	13	28
4A1C_3	5S_rRNA links to Rfam database...	0.74	0.56	1.00	30	7110	0	0	0	0	24
4AOB_A	SAM links to Rfam database...	0.58	0.40	0.85	17	4351	4	0	3	1	25
4ENB_A	crcB links to Rfam database...	0.60	0.37	1.00	7	1268	0	0	0	0	12
4ENC_A	crcB links to Rfam database...	0.76	0.58	1.00	11	1315	0	0	0	0	8

Performance of PPfold(seed) - scored lower in this pairwise comparison

1. Total counts & total scores for PPfold(seed)

Total Base Pair Counts
Total TP	1
Total TN	35018
Total FP	23
Total FP CONTRA	0
Total FP INCONS	4
Total FP COMP	19
Total FN	269

Total Scores
MCC	0.026
Average MCC ± 95% Confidence Intervals	0.010 ± 0.023
Sensitivity	0.004
Positive Predictive Value	0.200
Nr of predictions	8

2. Individual counts for PPfold(seed) [ download as .csv ]

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
3AMU_B	tRNA links to Rfam database...	0.00	0.00	0.00	0	3003	0	0	0	0	27
3RKF_A	Purine links to Rfam database...	0.00	0.00	0.00	0	2211	0	0	0	0	34
3SD1_A	THF links to Rfam database...	0.00	0.00	0.00	0	3916	0	0	0	0	42
4A1C_2	5_8S_rRNA links to Rfam database...	0.08	0.03	0.20	1	11776	23	0	4	19	32
4A1C_3	5S_rRNA links to Rfam database...	0.00	0.00	0.00	0	7140	0	0	0	0	54
4AOB_A	SAM links to Rfam database...	0.00	0.00	0.00	0	4371	0	0	0	0	42
4ENB_A	crcB links to Rfam database...	0.00	0.00	0.00	0	1275	0	0	0	0	19
4ENC_A	crcB links to Rfam database...	0.00	0.00	0.00	0	1326	0	0	0	0	19

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