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 RNAalifold(seed) - scored higher in this pairwise comparison

Total counts & total scores
Individual counts

Performance of TurboFold(20) - scored lower in this pairwise comparison

Total counts & total scores
Individual counts

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

Overview

Metric	RNAalifold(seed)		TurboFold(20)
MCC	0.591	>	0.590
Average MCC ± 95% Confidence Intervals	0.576 ± 0.092	<	0.621 ± 0.213
Sensitivity	0.383	<	0.469
Positive Predictive Value	0.920	>	0.748
Total TP	80	<	98
Total TN	25783	>	25739
Total FP	10	<	43
Total FP CONTRA	2	<	3
Total FP INCONS	5	<	30
Total FP COMP	3	<	10
Total FN	129	>	111
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	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

Performance of TurboFold(20) - scored lower in this pairwise comparison

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

Total Base Pair Counts
Total TP	98
Total TN	25739
Total FP	43
Total FP CONTRA	3
Total FP INCONS	30
Total FP COMP	10
Total FN	111

Total Scores
MCC	0.590
Average MCC ± 95% Confidence Intervals	0.621 ± 0.213
Sensitivity	0.469
Positive Predictive Value	0.748
Nr of predictions	7

2. Individual counts for TurboFold(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...	0.92	0.90	0.95	18	971	1	0	1	0	2
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...	0.59	0.48	0.74	20	3889	7	1	6	0	22
4A1C_2	5_8S_rRNA links to Rfam database...	0.18	0.15	0.21	5	11757	28	0	19	9	28
4AOB_A	SAM links to Rfam database...	0.56	0.40	0.77	17	4349	6	1	4	1	25
4ENB_A	crcB links to Rfam database...	0.69	0.47	1.00	9	1266	0	0	0	0	10
4ENC_A	crcB links to Rfam database...	0.65	0.47	0.90	9	1316	1	1	0	0	10

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