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 PETfold_pre2.0(seed) - scored higher in this pairwise comparison

Total counts & total scores
Individual counts

Performance of RNAfold - scored lower in this pairwise comparison

Total counts & total scores
Individual counts

Compile and download dataset for PETfold_pre2.0(seed) & RNAfold [.zip] - may take several seconds...

Overview

Metric	PETfold_pre2.0(seed)		RNAfold
MCC	0.680	>	0.515
Average MCC ± 95% Confidence Intervals	0.632 ± 0.134	>	0.524 ± 0.175
Sensitivity	0.551	>	0.441
Positive Predictive Value	0.843	>	0.609
Total TP	140	>	112
Total TN	33612	>	33594
Total FP	34	<	84
Total FP CONTRA	3	<	10
Total FP INCONS	23	<	62
Total FP COMP	8	<	12
Total FN	114	<	142
P-value	0.0

Performance plots

Performance of PETfold_pre2.0(seed) - scored higher in this pairwise comparison

1. Total counts & total scores for PETfold_pre2.0(seed)

Total Base Pair Counts
Total TP	140
Total TN	33612
Total FP	34
Total FP CONTRA	3
Total FP INCONS	23
Total FP COMP	8
Total FN	114

Total Scores
MCC	0.680
Average MCC ± 95% Confidence Intervals	0.632 ± 0.134
Sensitivity	0.551
Positive Predictive Value	0.843
Nr of predictions	8

2. Individual counts for PETfold_pre2.0(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...	0.40	0.30	0.55	6	1529	5	0	5	0	14
3J16_L	tRNA links to Rfam database...	0.82	0.70	0.95	21	2753	1	0	1	0	9
3UZL_B	tRNA links to Rfam database...	0.72	0.54	0.95	20	3549	2	1	0	1	17
4A1C_3	5S_rRNA links to Rfam database...	0.83	0.70	0.97	38	7101	1	0	1	0	16
4A1C_2	5_8S_rRNA links to Rfam database...	0.57	0.45	0.71	15	11760	12	0	6	6	18
4AOB_A	SAM links to Rfam database...	0.72	0.57	0.92	24	4345	3	0	2	1	18
4ENB_A	crcB links to Rfam database...	0.50	0.42	0.62	8	1262	5	1	4	0	11
4ENC_A	crcB links to Rfam database...	0.50	0.42	0.62	8	1313	5	1	4	0	11

Performance of RNAfold - scored lower in this pairwise comparison

1. Total counts & total scores for RNAfold

Total Base Pair Counts
Total TP	112
Total TN	33594
Total FP	84
Total FP CONTRA	10
Total FP INCONS	62
Total FP COMP	12
Total FN	142

Total Scores
MCC	0.515
Average MCC ± 95% Confidence Intervals	0.524 ± 0.175
Sensitivity	0.441
Positive Predictive Value	0.609
Nr of predictions	8

2. Individual counts for RNAfold [ 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...	0.61	0.55	0.69	11	1524	5	0	5	0	9
3J16_L	tRNA links to Rfam database...	0.75	0.57	1.00	17	2758	0	0	0	0	13
3UZL_B	tRNA links to Rfam database...	0.48	0.38	0.61	14	3547	9	0	9	0	23
4A1C_3	5S_rRNA links to Rfam database...	0.70	0.59	0.82	32	7101	7	1	6	0	22
4A1C_2	5_8S_rRNA links to Rfam database...	0.14	0.15	0.14	5	11744	43	5	27	11	28
4AOB_A	SAM links to Rfam database...	0.50	0.40	0.63	17	4344	11	2	8	1	25
4ENB_A	crcB links to Rfam database...	0.70	0.58	0.85	11	1262	2	1	1	0	8
4ENC_A	crcB links to Rfam database...	0.32	0.26	0.42	5	1314	7	1	6	0	14

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