CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

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Overview

Metric	PETfold_pre2.0(20)		CMfinder(20)
MCC	0.849	>	0.648
Average MCC ± 95% Confidence Intervals	0.806 ± 0.144	>	0.625 ± 0.138
Sensitivity	0.846	>	0.563
Positive Predictive Value	0.855	>	0.754
Total TP	230	>	153
Total TN	25961	<	26027
Total FP	90	>	71
Total FP CONTRA	11	<	15
Total FP INCONS	28	<	35
Total FP COMP	51	>	21
Total FN	42	<	119
P-value	1.34193807955e-08

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Performance plots

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

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

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

Total Base Pair Counts
Total TP	230
Total TN	25961
Total FP	90
Total FP CONTRA	11
Total FP INCONS	28
Total FP COMP	51
Total FN	42

Total Scores
MCC	0.849
Average MCC ± 95% Confidence Intervals	0.806 ± 0.144
Sensitivity	0.846
Positive Predictive Value	0.855
Nr of predictions	11

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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
3J20_0	tRNA links to Rfam database...	0.95	0.95	0.95	20	1198	1	1	0	0	1
3J2L_3	5S_rRNA links to Rfam database...	0.97	0.94	1.00	32	2988	4	0	0	4	2
3J3D_C	tRNA links to Rfam database...	0.87	0.89	0.85	17	948	3	3	0	0	2
3J3E_7	5S_rRNA links to Rfam database...	0.94	0.94	0.94	32	2707	7	0	2	5	2
3J3E_8	5_8S_rRNA links to Rfam database...	0.48	0.47	0.50	7	2728	11	2	5	4	8
3J3F_7	5S_rRNA links to Rfam database...	0.93	0.92	0.94	33	2899	6	0	2	4	3
3J3F_8	5_8S_rRNA links to Rfam database...	0.34	0.37	0.32	7	4739	24	5	10	9	12
3J3V_B	5S_rRNA links to Rfam database...	0.90	0.89	0.92	24	2630	11	0	2	9	3
3ZEX_D	5S_rRNA links to Rfam database...	0.93	0.91	0.94	32	2762	6	0	2	4	3
3ZND_W	tRNA links to Rfam database...	0.67	0.75	0.60	6	1181	15	0	4	11	2
4FRG_B	AdoCbl-variant links to Rfam database...	0.89	0.83	0.95	20	1181	2	0	1	1	4

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

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

Total Base Pair Counts
Total TP	153
Total TN	26027
Total FP	71
Total FP CONTRA	15
Total FP INCONS	35
Total FP COMP	21
Total FN	119

Total Scores
MCC	0.648
Average MCC ± 95% Confidence Intervals	0.625 ± 0.138
Sensitivity	0.563
Positive Predictive Value	0.754
Nr of predictions	11

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2. Individual counts for CMfinder(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...	0.84	0.76	0.94	16	1202	2	1	0	1	5
3J2L_3	5S_rRNA links to Rfam database...	0.57	0.50	0.65	17	2994	11	2	7	2	17
3J3D_C	tRNA links to Rfam database...	0.81	0.79	0.83	15	950	3	3	0	0	4
3J3E_7	5S_rRNA links to Rfam database...	0.81	0.74	0.89	25	2713	5	0	3	2	9
3J3E_8	5_8S_rRNA links to Rfam database...	0.14	0.13	0.17	2	2730	10	3	7	0	13
3J3F_7	5S_rRNA links to Rfam database...	0.79	0.72	0.87	26	2904	6	1	3	2	10
3J3F_8	5_8S_rRNA links to Rfam database...	0.48	0.47	0.50	9	4743	11	5	4	2	10
3J3V_B	5S_rRNA links to Rfam database...	0.53	0.41	0.69	11	2640	6	0	5	1	16
3ZEX_D	5S_rRNA links to Rfam database...	0.70	0.54	0.90	19	2775	3	0	2	1	16
3ZND_W	tRNA links to Rfam database...	0.67	0.75	0.60	6	1181	14	0	4	10	2
4FRG_B	AdoCbl-variant links to Rfam database...	0.54	0.29	1.00	7	1195	0	0	0	0	17

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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 PETfold_pre2.0(20) - scored higher 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 ]

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

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

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