CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

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Overview

Metric	Carnac(seed)		Mastr(seed)
MCC	0.179	>	0.033
Average MCC ± 95% Confidence Intervals	0.078 ± 0.093	>	0.007 ± 0.014
Sensitivity	0.032	>	0.003
Positive Predictive Value	1.000	>	0.375
Total TP	33	>	3
Total TN	166202	<	166227
Total FP	0	<	5
Total FP CONTRA	0	=	0
Total FP INCONS	0	<	5
Total FP COMP	0	=	0
Total FN	986	<	1016
P-value	5.06544643719e-08

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Performance plots

Comparison of performance of Carnac(seed) and Mastr(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 Carnac(seed) and Mastr(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 Carnac(seed) and Mastr(seed)).
Comparison of average Matthews Correlation Coefficients (MCCs) for Carnac(seed) and Mastr(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 Carnac(seed) and Mastr(seed)).

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

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

Total Base Pair Counts
Total TP	33
Total TN	166202
Total FP	0
Total FP CONTRA	0
Total FP INCONS	0
Total FP COMP	0
Total FN	986

Total Scores
MCC	0.179
Average MCC ± 95% Confidence Intervals	0.078 ± 0.093
Sensitivity	0.032
Positive Predictive Value	1.000
Nr of predictions	28

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2. Individual counts for Carnac(seed) [ 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
2LC8_A	GP_knot1 links to Rfam database...	0.44	0.20	1.00	4	1536	0	0	0	0	16
3A3A_A	tRNA-Sec links to Rfam database...	0.00	0.00	0.00	0	3655	0	0	0	0	37
3GX2_A	SAM links to Rfam database...	0.00	0.00	0.00	0	4371	0	0	0	0	40
3IVN_B	Purine links to Rfam database...	0.00	0.00	0.00	0	2346	0	0	0	0	31
3IZF_C	5S_rRNA links to Rfam database...	0.00	0.00	0.00	0	6903	0	0	0	0	54
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...	0.00	0.00	0.00	0	12246	0	0	0	0	36
3JYX_3	5S_rRNA links to Rfam database...	0.00	0.00	0.00	0	6328	0	0	0	0	27
3JYX_4	5_8S_rRNA links to Rfam database...	0.00	0.00	0.00	0	12246	0	0	0	0	33
3LA5_A	Purine links to Rfam database...	0.00	0.00	0.00	0	2485	0	0	0	0	34
3NPB_A	SAM links to Rfam database...	0.00	0.00	0.00	0	7021	0	0	0	0	46
3O58_3	5_8S_rRNA links to Rfam database...	0.00	0.00	0.00	0	12403	0	0	0	0	35
3O58_2	5S_rRNA links to Rfam database...	0.00	0.00	0.00	0	7260	0	0	0	0	38
3PDR_A	ykoK links to Rfam database...	0.00	0.00	0.00	0	12880	0	0	0	0	72
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
3W1K_J	tRNA-Sec links to Rfam database...	0.00	0.00	0.00	0	4186	0	0	0	0	38
3W3S_B	tRNA-Sec links to Rfam database...	0.00	0.00	0.00	0	4753	0	0	0	0	40
3ZEX_C	5_8S_rRNA links to Rfam database...	0.00	0.00	0.00	0	14196	0	0	0	0	52
4A1C_2	5_8S_rRNA links to Rfam database...	0.00	0.00	0.00	0	11781	0	0	0	0	33
4A1C_3	5S_rRNA links to Rfam database...	0.00	0.00	0.00	0	7140	0	0	0	0	54
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
4FRN_A	AdoCbl-variant links to Rfam database...	0.00	0.00	0.00	0	5151	0	0	0	0	36
4JF2_A	preQ1-II links to Rfam database...	0.78	0.61	1.00	19	2831	0	0	0	0	12

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

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

Total Base Pair Counts
Total TP	3
Total TN	166227
Total FP	5
Total FP CONTRA	0
Total FP INCONS	5
Total FP COMP	0
Total FN	1016

Total Scores
MCC	0.033
Average MCC ± 95% Confidence Intervals	0.007 ± 0.014
Sensitivity	0.003
Positive Predictive Value	0.375
Nr of predictions	28

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2. Individual counts for Mastr(seed) [ 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...	0.00	0.00	0.00	0	406	0	0	0	0	11
2LC8_A	GP_knot1 links to Rfam database...	0.00	0.00	0.00	0	1540	0	0	0	0	20
3A3A_A	tRNA-Sec links to Rfam database...	0.00	0.00	0.00	0	3655	0	0	0	0	37
3GX2_A	SAM links to Rfam database...	0.00	0.00	0.00	0	4371	0	0	0	0	40
3IVN_B	Purine links to Rfam database...	0.00	0.00	0.00	0	2346	0	0	0	0	31
3IZF_C	5S_rRNA links to Rfam database...	0.00	0.00	0.00	0	6903	0	0	0	0	54
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...	0.00	0.00	0.00	0	12246	0	0	0	0	36
3JYX_3	5S_rRNA links to Rfam database...	0.00	0.00	0.00	0	6328	0	0	0	0	27
3JYX_4	5_8S_rRNA links to Rfam database...	0.00	0.00	0.00	0	12246	0	0	0	0	33
3LA5_A	Purine links to Rfam database...	0.00	0.00	0.00	0	2485	0	0	0	0	34
3NPB_A	SAM links to Rfam database...	0.00	0.00	0.00	0	7021	0	0	0	0	46
3O58_3	5_8S_rRNA links to Rfam database...	0.00	0.00	0.00	0	12403	0	0	0	0	35
3O58_2	5S_rRNA links to Rfam database...	0.00	0.00	0.00	0	7260	0	0	0	0	38
3PDR_A	ykoK links to Rfam database...	0.00	0.00	0.00	0	12880	0	0	0	0	72
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
3W1K_J	tRNA-Sec links to Rfam database...	0.00	0.00	0.00	0	4186	0	0	0	0	38
3W3S_B	tRNA-Sec links to Rfam database...	0.00	0.00	0.00	0	4753	0	0	0	0	40
3ZEX_C	5_8S_rRNA links to Rfam database...	0.00	0.00	0.00	0	14196	0	0	0	0	52
4A1C_2	5_8S_rRNA links to Rfam database...	0.00	0.00	0.00	0	11781	0	0	0	0	33
4A1C_3	5S_rRNA links to Rfam database...	0.00	0.00	0.00	0	7140	0	0	0	0	54
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
4FRN_A	AdoCbl-variant links to Rfam database...	0.00	0.00	0.00	0	5151	0	0	0	0	36
4JF2_A	preQ1-II links to Rfam database...	0.19	0.10	0.38	3	2842	5	0	5	0	28

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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 Carnac(seed) - scored higher in this pairwise comparison

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

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

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

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

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