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 RNAalifold(seed) - scored higher in this pairwise comparison

Total counts & total scores
Individual counts

Performance of RNASLOpt - scored lower in this pairwise comparison

Total counts & total scores
Individual counts

Compile and download dataset for RNAalifold(seed) & RNASLOpt [.zip] - may take several seconds...

Overview

Metric	RNAalifold(seed)		RNASLOpt
MCC	0.472	>	0.390
Average MCC ± 95% Confidence Intervals	0.444 ± 0.347	<	0.473 ± 0.289
Sensitivity	0.293	<	0.323
Positive Predictive Value	0.765	>	0.478
Total TP	39	<	43
Total TN	20242	>	20203
Total FP	15	<	53
Total FP CONTRA	0	<	11
Total FP INCONS	12	<	36
Total FP COMP	3	<	6
Total FN	94	>	90
P-value	0.0

Performance plots

Performance of RNAalifold(seed) - scored higher in this pairwise comparison

1. Total counts & total scores for RNAalifold(seed)

Total Base Pair Counts
Total TP	39
Total TN	20242
Total FP	15
Total FP CONTRA	0
Total FP INCONS	12
Total FP COMP	3
Total FN	94

Total Scores
MCC	0.472
Average MCC ± 95% Confidence Intervals	0.444 ± 0.347
Sensitivity	0.293
Positive Predictive Value	0.765
Nr of predictions	5

2. Individual counts for RNAalifold(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...	-0.01	0.00	0.00	0	1528	12	0	12	0	20
4A1C_2	5_8S_rRNA links to Rfam database...	0.39	0.15	1.00	5	11776	2	0	0	2	28
4AOB_A	SAM links to Rfam database...	0.72	0.52	1.00	22	4349	1	0	0	1	20
4ENB_A	crcB links to Rfam database...	0.56	0.32	1.00	6	1269	0	0	0	0	13
4ENC_A	crcB links to Rfam database...	0.56	0.32	1.00	6	1320	0	0	0	0	13

Performance of RNASLOpt - scored lower in this pairwise comparison

1. Total counts & total scores for RNASLOpt

Total Base Pair Counts
Total TP	43
Total TN	20203
Total FP	53
Total FP CONTRA	11
Total FP INCONS	36
Total FP COMP	6
Total FN	90

Total Scores
MCC	0.390
Average MCC ± 95% Confidence Intervals	0.473 ± 0.289
Sensitivity	0.323
Positive Predictive Value	0.478
Nr of predictions	5

2. Individual counts for RNASLOpt [ 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...	0.47	0.35	0.64	7	1529	4	0	4	0	13
4A1C_2	5_8S_rRNA links to Rfam database...	0.23	0.24	0.22	8	11744	35	8	21	6	25
4AOB_A	SAM links to Rfam database...	0.26	0.19	0.38	8	4350	13	2	11	0	34
4ENB_A	crcB links to Rfam database...	0.76	0.58	1.00	11	1264	0	0	0	0	8
4ENC_A	crcB links to Rfam database...	0.65	0.47	0.90	9	1316	1	1	0	0	10

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