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 PPfold(20) - 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 PPfold(20) & RNASLOpt [.zip] - may take several seconds...

Overview

Metric	PPfold(20)		RNASLOpt
MCC	0.616	>	0.467
Average MCC ± 95% Confidence Intervals	0.572 ± 0.277	>	0.514 ± 0.309
Sensitivity	0.473	>	0.383
Positive Predictive Value	0.806	>	0.577
Total TP	79	>	64
Total TN	25795	>	25782
Total FP	24	<	53
Total FP CONTRA	0	<	11
Total FP INCONS	19	<	36
Total FP COMP	5	<	6
Total FN	88	<	103
P-value	0.0

Performance plots

Performance of PPfold(20) - scored higher in this pairwise comparison

1. Total counts & total scores for PPfold(20)

Total Base Pair Counts
Total TP	79
Total TN	25795
Total FP	24
Total FP CONTRA	0
Total FP INCONS	19
Total FP COMP	5
Total FN	88

Total Scores
MCC	0.616
Average MCC ± 95% Confidence Intervals	0.572 ± 0.277
Sensitivity	0.473
Positive Predictive Value	0.806
Nr of predictions	5

2. Individual counts for PPfold(20) [ download as .csv ]

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
4A1C_3	5S_rRNA links to Rfam database...	0.77	0.63	0.94	34	7104	2	0	2	0	20
4A1C_2	5_8S_rRNA links to Rfam database...	0.21	0.15	0.29	5	11764	16	0	12	4	28
4AOB_A	SAM links to Rfam database...	0.74	0.60	0.93	25	4344	3	0	2	1	17
4ENB_A	crcB links to Rfam database...	0.56	0.37	0.88	7	1267	1	0	1	0	12
4ENC_A	crcB links to Rfam database...	0.58	0.42	0.80	8	1316	2	0	2	0	11

Performance of RNASLOpt - scored lower in this pairwise comparison

1. Total counts & total scores for RNASLOpt

Total Base Pair Counts
Total TP	64
Total TN	25782
Total FP	53
Total FP CONTRA	11
Total FP INCONS	36
Total FP COMP	6
Total FN	103

Total Scores
MCC	0.467
Average MCC ± 95% Confidence Intervals	0.514 ± 0.309
Sensitivity	0.383
Positive Predictive Value	0.577
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
4A1C_3	5S_rRNA links to Rfam database...	0.67	0.52	0.88	28	7108	4	0	4	0	26
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.