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 CRWrnafold - scored higher in this pairwise comparison

Total counts & total scores
Individual counts

Performance of MXScarna(20) - scored lower in this pairwise comparison

Total counts & total scores
Individual counts

Compile and download dataset for CRWrnafold & MXScarna(20) [.zip] - may take several seconds...

Overview

Metric	CRWrnafold		MXScarna(20)
MCC	0.668	>	0.666
Average MCC ± 95% Confidence Intervals	0.692 ± 0.219	>	0.631 ± 0.257
Sensitivity	0.683	>	0.634
Positive Predictive Value	0.663	<	0.707
Total TP	112	>	104
Total TN	12205	<	12227
Total FP	83	>	74
Total FP CONTRA	18	>	16
Total FP INCONS	39	>	27
Total FP COMP	26	<	31
Total FN	52	<	60
P-value	0.0

Performance plots

Comparison of performance of CRWrnafold and MXScarna(20). Positive Predictive Value (PPV) is plotted against sensitivity. Each dot represents a single test of each method. See tables below for raw data (individual counts for CRWrnafold and MXScarna(20)).
Comparison of average Matthews Correlation Coefficients (MCCs) for CRWrnafold and MXScarna(20). The whiskers correspond to 95% confidence intervals (CIs). 'n' denotes the number of MCCs used to calculate average MCCs and CIs. See tables below for raw data (individual counts for CRWrnafold and MXScarna(20)).

Performance of CRWrnafold - scored higher in this pairwise comparison

1. Total counts & total scores for CRWrnafold

Total Base Pair Counts
Total TP	112
Total TN	12205
Total FP	83
Total FP CONTRA	18
Total FP INCONS	39
Total FP COMP	26
Total FN	52

Total Scores
MCC	0.668
Average MCC ± 95% Confidence Intervals	0.692 ± 0.219
Sensitivity	0.683
Positive Predictive Value	0.663
Nr of predictions	7

2. Individual counts for CRWrnafold [ download as .csv ]

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
3AMU_B	tRNA links to Rfam database...	0.77	0.79	0.75	15	1137	8	0	5	3	4
3SD1_A	THF links to Rfam database...	0.63	0.66	0.61	19	1502	12	6	6	0	10
4A1C_3	5S_rRNA links to Rfam database...	0.85	0.84	0.86	31	2727	7	0	5	2	6
4A1C_2	5_8S_rRNA links to Rfam database...	0.19	0.25	0.15	5	4483	44	8	20	16	15
4AOB_A	SAM links to Rfam database...	0.71	0.69	0.74	20	1410	8	4	3	1	9
4ENB_A	crcB links to Rfam database...	0.85	0.73	1.00	11	461	2	0	0	2	4
4ENC_A	crcB links to Rfam database...	0.85	0.73	1.00	11	485	2	0	0	2	4

Performance of MXScarna(20) - scored lower in this pairwise comparison

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

Total Base Pair Counts
Total TP	104
Total TN	12227
Total FP	74
Total FP CONTRA	16
Total FP INCONS	27
Total FP COMP	31
Total FN	60

Total Scores
MCC	0.666
Average MCC ± 95% Confidence Intervals	0.631 ± 0.257
Sensitivity	0.634
Positive Predictive Value	0.707
Nr of predictions	7

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

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
3AMU_B	tRNA links to Rfam database...	1.00	1.00	1.00	19	1138	3	0	0	3	0
3SD1_A	THF links to Rfam database...	0.74	0.76	0.73	22	1503	9	6	2	1	7
4A1C_3	5S_rRNA links to Rfam database...	0.80	0.78	0.83	29	2728	12	0	6	6	8
4A1C_2	5_8S_rRNA links to Rfam database...	0.22	0.25	0.21	5	4492	36	8	11	17	15
4AOB_A	SAM links to Rfam database...	0.68	0.69	0.69	20	1408	13	2	7	4	9
4ENB_A	crcB links to Rfam database...	0.29	0.13	0.67	2	469	1	0	1	0	13
4ENC_A	crcB links to Rfam database...	0.68	0.47	1.00	7	489	0	0	0	0	8

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