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(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 RNAalifold(20) & PPfold(seed) [.zip] - may take several seconds...

Overview

Metric	RNAalifold(20)		PPfold(seed)
MCC	0.627	>	0.026
Average MCC ± 95% Confidence Intervals	0.612 ± 0.181	>	0.010 ± 0.023
Sensitivity	0.481	>	0.004
Positive Predictive Value	0.823	>	0.200
Total TP	130	>	1
Total TN	34865	<	35018
Total FP	32	>	23
Total FP CONTRA	3	>	0
Total FP INCONS	25	>	4
Total FP COMP	4	<	19
Total FN	140	<	269
P-value	0.0

Performance plots

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

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

Total Base Pair Counts
Total TP	130
Total TN	34865
Total FP	32
Total FP CONTRA	3
Total FP INCONS	25
Total FP COMP	4
Total FN	140

Total Scores
MCC	0.627
Average MCC ± 95% Confidence Intervals	0.612 ± 0.181
Sensitivity	0.481
Positive Predictive Value	0.823
Nr of predictions	8

2. Individual counts for RNAalifold(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...	0.86	0.74	1.00	20	2983	1	0	0	1	7
3RKF_A	Purine links to Rfam database...	0.68	0.50	0.94	17	2193	1	0	1	0	17
3SD1_A	THF links to Rfam database...	0.70	0.60	0.83	25	3886	5	1	4	0	17
4A1C_2	5_8S_rRNA links to Rfam database...	0.17	0.15	0.19	5	11755	23	2	19	2	28
4A1C_3	5S_rRNA links to Rfam database...	0.74	0.57	0.97	31	7108	1	0	1	0	23
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...	0.46	0.21	1.00	4	1271	0	0	0	0	15
4ENC_A	crcB links to Rfam database...	0.56	0.32	1.00	6	1320	0	0	0	0	13

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.