CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

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Overview

Metric	MXScarna(20)		Alterna
MCC	0.724	>	0.571
Average MCC ± 95% Confidence Intervals	0.728 ± 0.081	>	0.603 ± 0.155
Sensitivity	0.601	>	0.504
Positive Predictive Value	0.879	>	0.656
Total TP	218	>	183
Total TN	35516	>	35485
Total FP	42	<	118
Total FP CONTRA	9	<	11
Total FP INCONS	21	<	85
Total FP COMP	12	<	22
Total FN	145	<	180
P-value	1.61358433984e-08

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Performance plots

Comparison of performance of MXScarna(20) and Alterna. 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 MXScarna(20) and Alterna).
Comparison of performance of MXScarna(20) and Alterna. 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 MXScarna(20) and Alterna).
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 MXScarna(20) and Alterna).
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 MXScarna(20) and Alterna).
Comparison of average Matthews Correlation Coefficients (MCCs) for MXScarna(20) and Alterna. 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 MXScarna(20) and Alterna).
Comparison of average Matthews Correlation Coefficients (MCCs) for MXScarna(20) and Alterna. 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 MXScarna(20) and Alterna).

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

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

Total Base Pair Counts
Total TP	218
Total TN	35516
Total FP	42
Total FP CONTRA	9
Total FP INCONS	21
Total FP COMP	12
Total FN	145

Total Scores
MCC	0.724
Average MCC ± 95% Confidence Intervals	0.728 ± 0.081
Sensitivity	0.601
Positive Predictive Value	0.879
Nr of predictions	13

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

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2KDQ_B	mir-TAR links to Rfam database...	0.95	0.91	1.00	10	396	0	0	0	0	1
2L94_A	HIV_FE links to Rfam database...	0.73	0.70	0.78	14	972	4	0	4	0	6
2WRQ_Y	tRNA links to Rfam database...	0.57	0.59	0.56	10	2832	13	5	3	5	7
2XKV_B	Bacteria_small_SRP links to Rfam database...	0.45	0.20	1.00	4	4556	3	0	0	3	16
2XQD_Y	tRNA links to Rfam database...	0.88	0.78	1.00	21	2829	0	0	0	0	6
3A2K_C	tRNA links to Rfam database...	0.66	0.57	0.76	16	2905	6	1	4	1	12
3AMU_B	tRNA links to Rfam database...	0.86	0.74	1.00	20	2983	2	0	0	2	7
3GX2_A	SAM links to Rfam database...	0.70	0.58	0.85	23	4344	5	0	4	1	17
3IVN_B	Purine links to Rfam database...	0.74	0.58	0.95	18	2327	1	1	0	0	13
3JYV_7	tRNA links to Rfam database...	0.79	0.63	1.00	20	2830	0	0	0	0	12
3LA5_A	Purine links to Rfam database...	0.78	0.62	1.00	21	2464	0	0	0	0	13
3RKF_A	Purine links to Rfam database...	0.72	0.53	1.00	18	2193	0	0	0	0	16
3SD1_A	THF links to Rfam database...	0.63	0.55	0.74	23	3885	8	2	6	0	19

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Performance of Alterna - scored lower in this pairwise comparison

1. Total counts & total scores for Alterna

Total Base Pair Counts
Total TP	183
Total TN	35485
Total FP	118
Total FP CONTRA	11
Total FP INCONS	85
Total FP COMP	22
Total FN	180

Total Scores
MCC	0.571
Average MCC ± 95% Confidence Intervals	0.603 ± 0.155
Sensitivity	0.504
Positive Predictive Value	0.656
Nr of predictions	13

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

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2KDQ_B	mir-TAR links to Rfam database...	0.95	0.91	1.00	10	396	0	0	0	0	1
2L94_A	HIV_FE links to Rfam database...	0.97	0.95	1.00	19	971	0	0	0	0	1
2WRQ_Y	tRNA links to Rfam database...	0.57	0.59	0.56	10	2832	13	5	3	5	7
2XKV_B	Bacteria_small_SRP links to Rfam database...	0.45	0.45	0.45	9	4540	25	0	11	14	11
2XQD_Y	tRNA links to Rfam database...	0.67	0.59	0.76	16	2829	5	0	5	0	11
3A2K_C	tRNA links to Rfam database...	0.44	0.43	0.46	12	2900	14	2	12	0	16
3AMU_B	tRNA links to Rfam database...	0.64	0.59	0.70	16	2980	9	0	7	2	11
3GX2_A	SAM links to Rfam database...	0.47	0.40	0.57	16	4343	13	1	11	1	24
3IVN_B	Purine links to Rfam database...	0.74	0.61	0.90	19	2325	2	1	1	0	12
3JYV_7	tRNA links to Rfam database...	-0.01	0.00	0.00	0	2828	22	0	22	0	32
3LA5_A	Purine links to Rfam database...	0.78	0.62	1.00	21	2464	0	0	0	0	13
3RKF_A	Purine links to Rfam database...	0.69	0.56	0.86	19	2189	3	1	2	0	15
3SD1_A	THF links to Rfam database...	0.46	0.38	0.57	16	3888	12	1	11	0	26

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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 MXScarna(20) - scored higher in this pairwise comparison

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

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

Performance of Alterna - scored lower in this pairwise comparison

1. Total counts & total scores for Alterna

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