CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

Home

Methods

Datasets

Rankings

RNA 2D Atlas

Help

FAQ

Contact us

RSS feeds

Twitter

Overview

Metric	RDfolder		PPfold(seed)
MCC	0.371	>	0.121
Average MCC ± 95% Confidence Intervals	0.365 ± 0.171	>	0.047 ± 0.106
Sensitivity	0.281	>	0.020
Positive Predictive Value	0.503	<	0.750
Total TP	85	>	6
Total TN	27851	<	28012
Total FP	88	>	2
Total FP CONTRA	6	>	0
Total FP INCONS	78	>	2
Total FP COMP	4	>	0
Total FN	218	<	297
P-value	1.04628667909e-08

^top

Performance plots

Comparison of performance of RDfolder and PPfold(seed). 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 RDfolder and PPfold(seed)).
Comparison of performance of RDfolder and PPfold(seed). 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 RDfolder and PPfold(seed)).
Average Matthews Correlation Coefficients (MCC) with 95% confidence intervals (CIs) were plotted for different RNA families, for which at least 3 members were present in the benchmarking dataset. 'n' denotes the number of MCCs used to calculate the average and CI. See tables below for raw data (individual counts for RDfolder and PPfold(seed)).
Average Matthews Correlation Coefficients (MCC) with 95% confidence intervals (CIs) were plotted for different RNA families, for which at least 3 members were present in the benchmarking dataset. 'n' denotes the number of MCCs used to calculate the average and CI. See tables below for raw data (individual counts for RDfolder and PPfold(seed)).
Comparison of average Matthews Correlation Coefficients (MCCs) for RDfolder and PPfold(seed). 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 RDfolder and PPfold(seed)).
Comparison of average Matthews Correlation Coefficients (MCCs) for RDfolder and PPfold(seed). 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 RDfolder and PPfold(seed)).

^top

Performance of RDfolder - scored higher in this pairwise comparison

1. Total counts & total scores for RDfolder

Total Base Pair Counts
Total TP	85
Total TN	27851
Total FP	88
Total FP CONTRA	6
Total FP INCONS	78
Total FP COMP	4
Total FN	218

Total Scores
MCC	0.371
Average MCC ± 95% Confidence Intervals	0.365 ± 0.171
Sensitivity	0.281
Positive Predictive Value	0.503
Nr of predictions	10

^top

2. Individual counts for RDfolder [ 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	1526	14	2	12	0	20
3AMU_B	tRNA links to Rfam database...	0.18	0.15	0.22	4	2985	16	2	12	2	23
3J16_L	tRNA links to Rfam database...	0.22	0.17	0.31	5	2759	11	0	11	0	25
3J20_0	tRNA links to Rfam database...	0.73	0.57	0.94	17	2832	2	0	1	1	13
3RKF_A	Purine links to Rfam database...	0.76	0.59	1.00	20	2191	0	0	0	0	14
3SD1_A	THF links to Rfam database...	0.30	0.17	0.54	7	3903	6	0	6	0	35
3W3S_B	tRNA-Sec links to Rfam database...	0.27	0.23	0.33	9	4726	18	1	17	0	31
4AOB_A	SAM links to Rfam database...	0.35	0.26	0.48	11	4348	13	1	11	1	31
4ENB_A	crcB links to Rfam database...	0.43	0.32	0.60	6	1265	4	0	4	0	13
4ENC_A	crcB links to Rfam database...	0.43	0.32	0.60	6	1316	4	0	4	0	13

^top

Performance of PPfold(seed) - scored lower in this pairwise comparison

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

Total Base Pair Counts
Total TP	6
Total TN	28012
Total FP	2
Total FP CONTRA	0
Total FP INCONS	2
Total FP COMP	0
Total FN	297

Total Scores
MCC	0.121
Average MCC ± 95% Confidence Intervals	0.047 ± 0.106
Sensitivity	0.020
Positive Predictive Value	0.750
Nr of predictions	10

^top

2. Individual counts for PPfold(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...	0.47	0.30	0.75	6	1532	2	0	2	0	14
3AMU_B	tRNA links to Rfam database...	0.00	0.00	0.00	0	3003	0	0	0	0	27
3J16_L	tRNA links to Rfam database...	0.00	0.00	0.00	0	2775	0	0	0	0	30
3J20_0	tRNA links to Rfam database...	0.00	0.00	0.00	0	2850	0	0	0	0	30
3RKF_A	Purine links to Rfam database...	0.00	0.00	0.00	0	2211	0	0	0	0	34
3SD1_A	THF links to Rfam database...	0.00	0.00	0.00	0	3916	0	0	0	0	42
3W3S_B	tRNA-Sec links to Rfam database...	0.00	0.00	0.00	0	4753	0	0	0	0	40
4AOB_A	SAM links to Rfam database...	0.00	0.00	0.00	0	4371	0	0	0	0	42
4ENB_A	crcB links to Rfam database...	0.00	0.00	0.00	0	1275	0	0	0	0	19
4ENC_A	crcB links to Rfam database...	0.00	0.00	0.00	0	1326	0	0	0	0	19

^top

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

Table of contents:

Overview

Performance plots

Performance of RDfolder - scored higher in this pairwise comparison

1. Total counts & total scores for RDfolder

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

Performance of PPfold(seed) - scored lower in this pairwise comparison

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

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