CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

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Overview

Metric	RNAalifold(seed)		PETfold_pre2.0(20)
MCC	0.527	>	0.449
Average MCC ± 95% Confidence Intervals	0.484 ± 0.194	>	0.464 ± 0.188
Sensitivity	0.278	<	0.342
Positive Predictive Value	1.000	>	0.595
Total TP	74	<	91
Total TN	56110	>	56031
Total FP	3	<	85
Total FP CONTRA	0	<	1
Total FP INCONS	0	<	61
Total FP COMP	3	<	23
Total FN	192	>	175
P-value	0.0

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Performance plots

Comparison of performance of RNAalifold(seed) and PETfold_pre2.0(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 RNAalifold(seed) and PETfold_pre2.0(20)).
Comparison of performance of RNAalifold(seed) and PETfold_pre2.0(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 RNAalifold(seed) and PETfold_pre2.0(20)).
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 RNAalifold(seed) and PETfold_pre2.0(20)).
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 RNAalifold(seed) and PETfold_pre2.0(20)).
Comparison of average Matthews Correlation Coefficients (MCCs) for RNAalifold(seed) and PETfold_pre2.0(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 RNAalifold(seed) and PETfold_pre2.0(20)).
Comparison of average Matthews Correlation Coefficients (MCCs) for RNAalifold(seed) and PETfold_pre2.0(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 RNAalifold(seed) and PETfold_pre2.0(20)).

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

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

Total Base Pair Counts
Total TP	74
Total TN	56110
Total FP	3
Total FP CONTRA	0
Total FP INCONS	0
Total FP COMP	3
Total FN	192

Total Scores
MCC	0.527
Average MCC ± 95% Confidence Intervals	0.484 ± 0.194
Sensitivity	0.278
Positive Predictive Value	1.000
Nr of predictions	8

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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
3J3E_8	5_8S_rRNA links to Rfam database...	0.00	0.00	0.00	0	7503	0	0	0	0	33
3J3F_8	5_8S_rRNA links to Rfam database...	0.50	0.25	1.00	9	12237	0	0	0	0	27
3ZEX_C	5_8S_rRNA links to Rfam database...	0.42	0.17	1.00	9	14187	0	0	0	0	43
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
4FRG_B	AdoCbl-variant links to Rfam database...	0.73	0.53	1.00	17	3469	0	0	0	0	15

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Performance of PETfold_pre2.0(20) - scored lower in this pairwise comparison

1. Total counts & total scores for PETfold_pre2.0(20)

Total Base Pair Counts
Total TP	91
Total TN	56031
Total FP	85
Total FP CONTRA	1
Total FP INCONS	61
Total FP COMP	23
Total FN	175

Total Scores
MCC	0.449
Average MCC ± 95% Confidence Intervals	0.464 ± 0.188
Sensitivity	0.342
Positive Predictive Value	0.595
Nr of predictions	8

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2. Individual counts for PETfold_pre2.0(20) [ download as .csv ]

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
3J3E_8	5_8S_rRNA links to Rfam database...	0.32	0.21	0.50	7	7489	11	0	7	4	26
3J3F_8	5_8S_rRNA links to Rfam database...	0.30	0.25	0.38	9	12222	22	0	15	7	27
3ZEX_C	5_8S_rRNA links to Rfam database...	0.24	0.17	0.35	9	14170	18	0	17	1	43
4A1C_2	5_8S_rRNA links to Rfam database...	0.19	0.15	0.25	5	11761	25	0	15	10	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...	0.61	0.42	0.89	8	1266	1	0	1	0	11
4ENC_A	crcB links to Rfam database...	0.55	0.42	0.73	8	1315	3	0	3	0	11
4FRG_B	AdoCbl-variant links to Rfam database...	0.75	0.63	0.91	20	3464	2	1	1	0	12

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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 RNAalifold(seed) - scored higher in this pairwise comparison

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

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

Performance of PETfold_pre2.0(20) - scored lower in this pairwise comparison

1. Total counts & total scores for PETfold_pre2.0(20)

2. Individual counts for PETfold_pre2.0(20) [ download as .csv ]