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 Cylofold - scored lower in this pairwise comparison

Total counts & total scores
Individual counts

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

Overview

Metric	PETfold_pre2.0(seed)		Cylofold
MCC	0.651	>	0.601
Average MCC ± 95% Confidence Intervals	0.610 ± 0.172	<	0.651 ± 0.231
Sensitivity	0.521	>	0.497
Positive Predictive Value	0.821	>	0.735
Total TP	87	>	83
Total TN	14751	>	14744
Total FP	21	<	31
Total FP CONTRA	3	=	3
Total FP INCONS	16	<	27
Total FP COMP	2	>	1
Total FN	80	<	84
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	87
Total TN	14751
Total FP	21
Total FP CONTRA	3
Total FP INCONS	16
Total FP COMP	2
Total FN	80

Total Scores
MCC	0.651
Average MCC ± 95% Confidence Intervals	0.610 ± 0.172
Sensitivity	0.521
Positive Predictive Value	0.821
Nr of predictions	6

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
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 Cylofold - scored lower in this pairwise comparison

1. Total counts & total scores for Cylofold

Total Base Pair Counts
Total TP	83
Total TN	14744
Total FP	31
Total FP CONTRA	3
Total FP INCONS	27
Total FP COMP	1
Total FN	84

Total Scores
MCC	0.601
Average MCC ± 95% Confidence Intervals	0.651 ± 0.231
Sensitivity	0.497
Positive Predictive Value	0.735
Nr of predictions	6

2. Individual counts for Cylofold [ 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...	0.45	0.38	0.54	14	3544	12	1	11	0	23
4AOB_A	SAM links to Rfam database...	0.35	0.26	0.48	11	4348	13	1	11	1	31
4ENB_A	crcB links to Rfam database...	0.89	0.79	1.00	15	1260	0	0	0	0	4
4ENC_A	crcB links to Rfam database...	0.86	0.79	0.94	15	1310	1	1	0	0	4

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