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 NanoFolder - scored lower in this pairwise comparison

Total counts & total scores
Individual counts

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

Overview

Metric	PETfold_pre2.0(seed)		NanoFolder
MCC	0.694	>	0.346
Average MCC ± 95% Confidence Intervals	0.651 ± 0.151	>	0.374 ± 0.176
Sensitivity	0.562	>	0.353
Positive Predictive Value	0.863	>	0.349
Total TP	132	>	83
Total TN	32350	>	32265
Total FP	29	<	165
Total FP CONTRA	2	<	21
Total FP INCONS	19	<	134
Total FP COMP	8	<	10
Total FN	103	<	152
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	132
Total TN	32350
Total FP	29
Total FP CONTRA	2
Total FP INCONS	19
Total FP COMP	8
Total FN	103

Total Scores
MCC	0.694
Average MCC ± 95% Confidence Intervals	0.651 ± 0.151
Sensitivity	0.562
Positive Predictive Value	0.863
Nr of predictions	7

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
4ENC_A	crcB links to Rfam database...	0.50	0.42	0.62	8	1313	5	1	4	0	11

Performance of NanoFolder - scored lower in this pairwise comparison

1. Total counts & total scores for NanoFolder

Total Base Pair Counts
Total TP	83
Total TN	32265
Total FP	165
Total FP CONTRA	21
Total FP INCONS	134
Total FP COMP	10
Total FN	152

Total Scores
MCC	0.346
Average MCC ± 95% Confidence Intervals	0.374 ± 0.176
Sensitivity	0.353
Positive Predictive Value	0.349
Nr of predictions	7

2. Individual counts for NanoFolder [ 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...	0.52	0.55	0.50	11	1518	11	0	11	0	9
3J16_L	tRNA links to Rfam database...	0.36	0.37	0.37	11	2745	19	3	16	0	19
3UZL_B	tRNA links to Rfam database...	0.36	0.35	0.38	13	3536	21	3	18	0	24
4A1C_3	5S_rRNA links to Rfam database...	0.48	0.46	0.51	25	7091	24	2	22	0	29
4A1C_2	5_8S_rRNA links to Rfam database...	0.00	0.00	0.00	0	11728	61	12	41	8	33
4AOB_A	SAM links to Rfam database...	0.33	0.29	0.39	12	4340	20	1	18	1	30
4ENC_A	crcB links to Rfam database...	0.57	0.58	0.58	11	1307	9	0	8	1	8

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