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 PPfold(20) - scored higher in this pairwise comparison

Total counts & total scores
Individual counts

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

Total counts & total scores
Individual counts

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

Overview

Metric	PPfold(20)		RNAalifold(seed)
MCC	0.605	>	0.591
Average MCC ± 95% Confidence Intervals	0.589 ± 0.167	>	0.576 ± 0.092
Sensitivity	0.455	>	0.383
Positive Predictive Value	0.812	<	0.920
Total TP	95	>	80
Total TN	25753	<	25783
Total FP	27	>	10
Total FP CONTRA	0	<	2
Total FP INCONS	22	>	5
Total FP COMP	5	>	3
Total FN	114	<	129
P-value	0.0

Performance plots

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

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

Total Base Pair Counts
Total TP	95
Total TN	25753
Total FP	27
Total FP CONTRA	0
Total FP INCONS	22
Total FP COMP	5
Total FN	114

Total Scores
MCC	0.605
Average MCC ± 95% Confidence Intervals	0.589 ± 0.167
Sensitivity	0.455
Positive Predictive Value	0.812
Nr of predictions	7

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

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2L94_A	HIV_FE links to Rfam database...	0.63	0.45	0.90	9	980	1	0	1	0	11
3RKF_A	Purine links to Rfam database...	0.73	0.56	0.95	19	2191	1	0	1	0	15
3SD1_A	THF links to Rfam database...	0.68	0.52	0.88	22	3891	3	0	3	0	20
4A1C_2	5_8S_rRNA links to Rfam database...	0.21	0.15	0.29	5	11764	16	0	12	4	28
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...	0.56	0.37	0.88	7	1267	1	0	1	0	12
4ENC_A	crcB links to Rfam database...	0.58	0.42	0.80	8	1316	2	0	2	0	11

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

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

Total Base Pair Counts
Total TP	80
Total TN	25783
Total FP	10
Total FP CONTRA	2
Total FP INCONS	5
Total FP COMP	3
Total FN	129

Total Scores
MCC	0.591
Average MCC ± 95% Confidence Intervals	0.576 ± 0.092
Sensitivity	0.383
Positive Predictive Value	0.920
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
2L94_A	HIV_FE links to Rfam database...	0.59	0.40	0.89	8	981	1	0	1	0	12
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

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