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 Contrafold - scored lower in this pairwise comparison

Total counts & total scores
Individual counts

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

Overview

Metric	PETfold_pre2.0(seed)		Contrafold
MCC	0.680	>	0.525
Average MCC ± 95% Confidence Intervals	0.632 ± 0.134	>	0.540 ± 0.168
Sensitivity	0.551	>	0.441
Positive Predictive Value	0.843	>	0.633
Total TP	140	>	112
Total TN	33612	>	33601
Total FP	34	<	74
Total FP CONTRA	3	<	12
Total FP INCONS	23	<	53
Total FP COMP	8	<	9
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 Contrafold - scored lower in this pairwise comparison

1. Total counts & total scores for Contrafold

Total Base Pair Counts
Total TP	112
Total TN	33601
Total FP	74
Total FP CONTRA	12
Total FP INCONS	53
Total FP COMP	9
Total FN	142

Total Scores
MCC	0.525
Average MCC ± 95% Confidence Intervals	0.540 ± 0.168
Sensitivity	0.441
Positive Predictive Value	0.633
Nr of predictions	8

2. Individual counts for Contrafold [ 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...	0.45	0.35	0.58	7	1528	5	2	3	0	13
3J16_L	tRNA links to Rfam database...	0.46	0.40	0.55	12	2753	10	1	9	0	18
3UZL_B	tRNA links to Rfam database...	0.70	0.54	0.91	20	3548	2	0	2	0	17
4A1C_3	5S_rRNA links to Rfam database...	0.66	0.57	0.78	31	7100	9	1	8	0	23
4A1C_2	5_8S_rRNA links to Rfam database...	0.16	0.15	0.17	5	11751	33	5	20	8	28
4AOB_A	SAM links to Rfam database...	0.44	0.36	0.56	15	4344	13	1	11	1	27
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...	0.73	0.58	0.92	11	1314	1	1	0	0	8

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