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 ProbKnot - scored lower in this pairwise comparison

Total counts & total scores
Individual counts

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

Overview

Metric	PETfold_pre2.0(seed)		ProbKnot
MCC	0.680	>	0.466
Average MCC ± 95% Confidence Intervals	0.632 ± 0.134	>	0.450 ± 0.236
Sensitivity	0.551	>	0.421
Positive Predictive Value	0.843	>	0.525
Total TP	140	>	107
Total TN	33612	>	33574
Total FP	34	<	110
Total FP CONTRA	3	<	15
Total FP INCONS	23	<	82
Total FP COMP	8	<	13
Total FN	114	<	147
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 ProbKnot - scored lower in this pairwise comparison

1. Total counts & total scores for ProbKnot

Total Base Pair Counts
Total TP	107
Total TN	33574
Total FP	110
Total FP CONTRA	15
Total FP INCONS	82
Total FP COMP	13
Total FN	147

Total Scores
MCC	0.466
Average MCC ± 95% Confidence Intervals	0.450 ± 0.236
Sensitivity	0.421
Positive Predictive Value	0.525
Nr of predictions	8

2. Individual counts for ProbKnot [ 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...	-0.01	0.00	0.00	0	1525	15	2	13	0	20
3J16_L	tRNA links to Rfam database...	0.35	0.33	0.38	10	2749	16	1	15	0	20
3UZL_B	tRNA links to Rfam database...	0.73	0.62	0.85	23	3543	4	0	4	0	14
4A1C_3	5S_rRNA links to Rfam database...	0.73	0.61	0.87	33	7102	6	1	4	1	21
4A1C_2	5_8S_rRNA links to Rfam database...	0.13	0.15	0.12	5	11738	49	7	31	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...	0.73	0.58	0.92	11	1263	1	1	0	0	8
4ENC_A	crcB links to Rfam database...	0.45	0.42	0.50	8	1310	8	1	7	0	11

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