CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

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Overview

Metric	RNASampler(20)		PPfold(seed)
MCC	0.609	>	0.061
Average MCC ± 95% Confidence Intervals	0.631 ± 0.123	>	0.019 ± 0.031
Sensitivity	0.460	>	0.010
Positive Predictive Value	0.813	>	0.385
Total TP	234	>	5
Total TN	73089	<	73364
Total FP	77	>	45
Total FP CONTRA	2	>	0
Total FP INCONS	52	>	8
Total FP COMP	23	<	37
Total FN	275	<	504
P-value	1.59816551561e-08

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Performance plots

Comparison of performance of RNASampler(20) 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 RNASampler(20) and PPfold(seed)).
Comparison of performance of RNASampler(20) 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 RNASampler(20) 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 RNASampler(20) 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 RNASampler(20) and PPfold(seed)).
Comparison of average Matthews Correlation Coefficients (MCCs) for RNASampler(20) 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 RNASampler(20) and PPfold(seed)).
Comparison of average Matthews Correlation Coefficients (MCCs) for RNASampler(20) 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 RNASampler(20) and PPfold(seed)).

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

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

Total Base Pair Counts
Total TP	234
Total TN	73089
Total FP	77
Total FP CONTRA	2
Total FP INCONS	52
Total FP COMP	23
Total FN	275

Total Scores
MCC	0.609
Average MCC ± 95% Confidence Intervals	0.631 ± 0.123
Sensitivity	0.460
Positive Predictive Value	0.813
Nr of predictions	14

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2. Individual counts for RNASampler(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...	0.82	0.70	0.95	19	2983	3	0	1	2	8
3J20_1	tRNA links to Rfam database...	0.96	0.91	1.00	21	2905	0	0	0	0	2
3J20_0	tRNA links to Rfam database...	0.80	0.67	0.95	20	2829	2	0	1	1	10
3J2L_3	5S_rRNA links to Rfam database...	0.45	0.32	0.63	17	7848	12	1	9	2	36
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...	0.67	0.48	0.95	20	3895	1	0	1	0	22
3ZEX_C	5_8S_rRNA links to Rfam database...	0.27	0.19	0.38	10	14170	20	1	15	4	42
3ZEX_D	5S_rRNA links to Rfam database...	0.68	0.49	0.96	24	6996	1	0	1	0	25
4A1C_3	5S_rRNA links to Rfam database...	0.74	0.56	1.00	30	7110	0	0	0	0	24
4A1C_2	5_8S_rRNA links to Rfam database...	0.18	0.15	0.23	5	11759	30	0	17	13	28
4AOB_A	SAM links to Rfam database...	0.58	0.40	0.85	17	4351	4	0	3	1	25
4ENB_A	crcB links to Rfam database...	0.60	0.37	1.00	7	1268	0	0	0	0	12
4ENC_A	crcB links to Rfam database...	0.76	0.58	1.00	11	1315	0	0	0	0	8
4FRG_B	AdoCbl-variant links to Rfam database...	0.55	0.41	0.76	13	3469	4	0	4	0	19

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

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

Total Base Pair Counts
Total TP	5
Total TN	73364
Total FP	45
Total FP CONTRA	0
Total FP INCONS	8
Total FP COMP	37
Total FN	504

Total Scores
MCC	0.061
Average MCC ± 95% Confidence Intervals	0.019 ± 0.031
Sensitivity	0.010
Positive Predictive Value	0.385
Nr of predictions	14

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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
3AMU_B	tRNA links to Rfam database...	0.00	0.00	0.00	0	3003	0	0	0	0	27
3J20_1	tRNA links to Rfam database...	0.00	0.00	0.00	0	2926	0	0	0	0	23
3J20_0	tRNA links to Rfam database...	0.00	0.00	0.00	0	2850	0	0	0	0	30
3J2L_3	5S_rRNA links to Rfam database...	0.00	0.00	0.00	0	7875	0	0	0	0	53
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
3ZEX_C	5_8S_rRNA links to Rfam database...	0.20	0.08	0.50	4	14188	22	0	4	18	48
3ZEX_D	5S_rRNA links to Rfam database...	0.00	0.00	0.00	0	7021	0	0	0	0	49
4A1C_3	5S_rRNA links to Rfam database...	0.00	0.00	0.00	0	7140	0	0	0	0	54
4A1C_2	5_8S_rRNA links to Rfam database...	0.08	0.03	0.20	1	11776	23	0	4	19	32
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
4FRG_B	AdoCbl-variant links to Rfam database...	0.00	0.00	0.00	0	3486	0	0	0	0	32

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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 RNASampler(20) - scored higher in this pairwise comparison

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

2. Individual counts for RNASampler(20) [ 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 ]