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

Overview

Metric	Mastr(20)		RNASLOpt
MCC	0.488	>	0.467
Average MCC ± 95% Confidence Intervals	0.399 ± 0.320	<	0.514 ± 0.309
Sensitivity	0.305	<	0.383
Positive Predictive Value	0.785	>	0.577
Total TP	51	<	64
Total TN	25828	>	25782
Total FP	16	<	53
Total FP CONTRA	0	<	11
Total FP INCONS	14	<	36
Total FP COMP	2	<	6
Total FN	116	>	103
P-value	0.0

Performance plots

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

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

Total Base Pair Counts
Total TP	51
Total TN	25828
Total FP	16
Total FP CONTRA	0
Total FP INCONS	14
Total FP COMP	2
Total FN	116

Total Scores
MCC	0.488
Average MCC ± 95% Confidence Intervals	0.399 ± 0.320
Sensitivity	0.305
Positive Predictive Value	0.785
Nr of predictions	5

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

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
4A1C_2	5_8S_rRNA links to Rfam database...	0.00	0.00	0.00	0	11781	0	0	0	0	33
4A1C_3	5S_rRNA links to Rfam database...	0.70	0.59	0.84	32	7102	7	0	6	1	22
4AOB_A	SAM links to Rfam database...	0.39	0.26	0.58	11	4352	9	0	8	1	31
4ENB_A	crcB links to Rfam database...	0.39	0.16	1.00	3	1272	0	0	0	0	16
4ENC_A	crcB links to Rfam database...	0.51	0.26	1.00	5	1321	0	0	0	0	14

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_2	5_8S_rRNA links to Rfam database...	0.23	0.24	0.22	8	11744	35	8	21	6	25
4A1C_3	5S_rRNA links to Rfam database...	0.67	0.52	0.88	28	7108	4	0	4	0	26
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.