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 RNAalifold(seed) - 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 RNAalifold(seed) & IPknot [.zip] - may take several seconds...

Overview

Metric	RNAalifold(seed)		IPknot
MCC	0.523	>	0.505
Average MCC ± 95% Confidence Intervals	0.490 ± 0.224	<	0.521 ± 0.198
Sensitivity	0.344	<	0.402
Positive Predictive Value	0.800	>	0.641
Total TP	72	<	84
Total TN	26330	>	26289
Total FP	21	<	53
Total FP CONTRA	2	<	6
Total FP INCONS	16	<	41
Total FP COMP	3	<	6
Total FN	137	>	125
P-value	0.0

Performance plots

Performance of RNAalifold(seed) - scored higher in this pairwise comparison

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

Total Base Pair Counts
Total TP	72
Total TN	26330
Total FP	21
Total FP CONTRA	2
Total FP INCONS	16
Total FP COMP	3
Total FN	137

Total Scores
MCC	0.523
Average MCC ± 95% Confidence Intervals	0.490 ± 0.224
Sensitivity	0.344
Positive Predictive Value	0.800
Nr of predictions	7

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

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2LC8_A	GP_knot1 links to Rfam database...	-0.01	0.00	0.00	0	1528	12	0	12	0	20
3RKF_A	Purine links to Rfam database...	0.63	0.47	0.84	16	2192	3	1	2	0	18
3SD1_A	THF links to Rfam database...	0.58	0.40	0.85	17	3896	3	1	2	0	25
4A1C_2	5_8S_rRNA links to Rfam database...	0.39	0.15	1.00	5	11776	2	0	0	2	28
4AOB_A	SAM links to Rfam database...	0.72	0.52	1.00	22	4349	1	0	0	1	20
4ENB_A	crcB links to Rfam database...	0.56	0.32	1.00	6	1269	0	0	0	0	13
4ENC_A	crcB links to Rfam database...	0.56	0.32	1.00	6	1320	0	0	0	0	13

Performance of IPknot - scored lower in this pairwise comparison

1. Total counts & total scores for IPknot

Total Base Pair Counts
Total TP	84
Total TN	26289
Total FP	53
Total FP CONTRA	6
Total FP INCONS	41
Total FP COMP	6
Total FN	125

Total Scores
MCC	0.505
Average MCC ± 95% Confidence Intervals	0.521 ± 0.198
Sensitivity	0.402
Positive Predictive Value	0.641
Nr of predictions	7

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
2LC8_A	GP_knot1 links to Rfam database...	0.40	0.30	0.55	6	1529	5	1	4	0	14
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...	0.61	0.48	0.80	20	3891	5	0	5	0	22
4A1C_2	5_8S_rRNA links to Rfam database...	0.17	0.15	0.19	5	11755	26	4	17	5	28
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.