CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

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Overview

Metric	ContextFold		Carnac(20)
MCC	0.781	>	0.612
Average MCC ± 95% Confidence Intervals	0.762 ± 0.160	>	0.514 ± 0.203
Sensitivity	0.731	>	0.466
Positive Predictive Value	0.840	>	0.813
Total TP	204	>	130
Total TN	24164	<	24247
Total FP	74	>	41
Total FP CONTRA	13	>	4
Total FP INCONS	26	=	26
Total FP COMP	35	>	11
Total FN	75	<	149
P-value	1.19192530585e-08

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Performance plots

Comparison of performance of ContextFold and Carnac(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 ContextFold and Carnac(20)).
Comparison of performance of ContextFold and Carnac(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 ContextFold and Carnac(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 ContextFold and Carnac(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 ContextFold and Carnac(20)).
Comparison of average Matthews Correlation Coefficients (MCCs) for ContextFold and Carnac(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 ContextFold and Carnac(20)).
Comparison of average Matthews Correlation Coefficients (MCCs) for ContextFold and Carnac(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 ContextFold and Carnac(20)).

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Performance of ContextFold - scored higher in this pairwise comparison

1. Total counts & total scores for ContextFold

Total Base Pair Counts
Total TP	204
Total TN	24164
Total FP	74
Total FP CONTRA	13
Total FP INCONS	26
Total FP COMP	35
Total FN	75

Total Scores
MCC	0.781
Average MCC ± 95% Confidence Intervals	0.762 ± 0.160
Sensitivity	0.731
Positive Predictive Value	0.840
Nr of predictions	11

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

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
3J20_0	tRNA links to Rfam database...	0.95	0.95	0.95	20	1198	2	1	0	1	1
3J20_1	tRNA links to Rfam database...	1.00	1.00	1.00	20	1092	1	0	0	1	0
3J2L_3	5S_rRNA links to Rfam database...	0.95	0.91	1.00	31	2989	4	0	0	4	3
3ZEX_C	5_8S_rRNA links to Rfam database...	0.44	0.41	0.48	12	5349	23	4	9	10	17
3ZEX_D	5S_rRNA links to Rfam database...	0.92	0.86	1.00	30	2766	4	0	0	4	5
4A1C_2	5_8S_rRNA links to Rfam database...	0.26	0.25	0.28	5	4498	26	3	10	13	15
4A1C_3	5S_rRNA links to Rfam database...	0.96	0.92	1.00	34	2729	1	0	0	1	3
4AOB_A	SAM links to Rfam database...	0.62	0.59	0.68	17	1412	9	2	6	1	12
4ENB_A	crcB links to Rfam database...	0.77	0.60	1.00	9	463	0	0	0	0	6
4ENC_A	crcB links to Rfam database...	0.73	0.60	0.90	9	486	1	1	0	0	6
4FRG_B	AdoCbl-variant links to Rfam database...	0.77	0.71	0.85	17	1182	3	2	1	0	7

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

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

Total Base Pair Counts
Total TP	130
Total TN	24247
Total FP	41
Total FP CONTRA	4
Total FP INCONS	26
Total FP COMP	11
Total FN	149

Total Scores
MCC	0.612
Average MCC ± 95% Confidence Intervals	0.514 ± 0.203
Sensitivity	0.466
Positive Predictive Value	0.813
Nr of predictions	11

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

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
3J20_0	tRNA links to Rfam database...	0.69	0.71	0.68	15	1197	8	1	6	1	6
3J20_1	tRNA links to Rfam database...	0.89	0.80	1.00	16	1096	1	0	0	1	4
3J2L_3	5S_rRNA links to Rfam database...	0.59	0.53	0.67	18	2993	11	0	9	2	16
3ZEX_C	5_8S_rRNA links to Rfam database...	0.37	0.21	0.67	6	5365	4	1	2	1	23
3ZEX_D	5S_rRNA links to Rfam database...	0.81	0.66	1.00	23	2773	3	0	0	3	12
4A1C_2	5_8S_rRNA links to Rfam database...	0.42	0.25	0.71	5	4509	3	0	2	1	15
4A1C_3	5S_rRNA links to Rfam database...	0.79	0.73	0.87	27	2732	5	0	4	1	10
4AOB_A	SAM links to Rfam database...	0.59	0.48	0.74	14	1418	6	2	3	1	15
4ENB_A	crcB links to Rfam database...	0.00	0.00	0.00	0	472	0	0	0	0	15
4ENC_A	crcB links to Rfam database...	0.00	0.00	0.00	0	496	0	0	0	0	15
4FRG_B	AdoCbl-variant links to Rfam database...	0.50	0.25	1.00	6	1196	0	0	0	0	18

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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 ContextFold - scored higher in this pairwise comparison

1. Total counts & total scores for ContextFold

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

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

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

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