CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

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Overview

Metric	TurboFold(20)		Multilign(20)
MCC	0.796	>	0.699
Average MCC ± 95% Confidence Intervals	0.791 ± 0.111	>	0.684 ± 0.159
Sensitivity	0.762	>	0.688
Positive Predictive Value	0.838	>	0.718
Total TP	259	>	234
Total TN	22637	>	22620
Total FP	75	<	119
Total FP CONTRA	13	<	21
Total FP INCONS	37	<	71
Total FP COMP	25	<	27
Total FN	81	<	106
P-value	2.43573297697e-08

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Performance plots

Comparison of performance of TurboFold(20) and Multilign(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 TurboFold(20) and Multilign(20)).
Comparison of performance of TurboFold(20) and Multilign(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 TurboFold(20) and Multilign(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 TurboFold(20) and Multilign(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 TurboFold(20) and Multilign(20)).
Comparison of average Matthews Correlation Coefficients (MCCs) for TurboFold(20) and Multilign(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 TurboFold(20) and Multilign(20)).
Comparison of average Matthews Correlation Coefficients (MCCs) for TurboFold(20) and Multilign(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 TurboFold(20) and Multilign(20)).

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

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

Total Base Pair Counts
Total TP	259
Total TN	22637
Total FP	75
Total FP CONTRA	13
Total FP INCONS	37
Total FP COMP	25
Total FN	81

Total Scores
MCC	0.796
Average MCC ± 95% Confidence Intervals	0.791 ± 0.111
Sensitivity	0.762
Positive Predictive Value	0.838
Nr of predictions	14

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

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2L94_A	HIV_FE links to Rfam database...	0.94	0.94	0.94	17	339	2	0	1	1	1
3AMU_B	tRNA links to Rfam database...	0.81	0.79	0.83	15	1139	6	0	3	3	4
3J20_1	tRNA links to Rfam database...	1.00	1.00	1.00	20	1092	1	0	0	1	0
3J20_0	tRNA links to Rfam database...	0.74	0.76	0.73	16	1197	7	1	5	1	5
3J2L_3	5S_rRNA links to Rfam database...	0.92	0.91	0.94	31	2987	5	1	1	3	3
3RKF_A	Purine links to Rfam database...	0.91	0.83	1.00	20	846	0	0	0	0	4
3SD1_A	THF links to Rfam database...	0.71	0.69	0.74	20	1506	7	2	5	0	9
3ZEX_D	5S_rRNA links to Rfam database...	0.86	0.80	0.93	28	2766	6	0	2	4	7
4A1C_3	5S_rRNA links to Rfam database...	0.86	0.84	0.89	31	2728	6	0	4	2	6
4A1C_2	5_8S_rRNA links to Rfam database...	0.22	0.25	0.21	5	4492	28	6	13	9	15
4AOB_A	SAM links to Rfam database...	0.67	0.59	0.77	17	1415	6	2	3	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...	0.93	0.88	1.00	21	1181	0	0	0	0	3

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

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

Total Base Pair Counts
Total TP	234
Total TN	22620
Total FP	119
Total FP CONTRA	21
Total FP INCONS	71
Total FP COMP	27
Total FN	106

Total Scores
MCC	0.699
Average MCC ± 95% Confidence Intervals	0.684 ± 0.159
Sensitivity	0.688
Positive Predictive Value	0.718
Nr of predictions	14

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

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2L94_A	HIV_FE links to Rfam database...	1.00	1.00	1.00	18	339	1	0	0	1	0
3AMU_B	tRNA links to Rfam database...	0.71	0.74	0.70	14	1137	9	0	6	3	5
3J20_1	tRNA links to Rfam database...	1.00	1.00	1.00	20	1092	1	0	0	1	0
3J20_0	tRNA links to Rfam database...	0.68	0.71	0.65	15	1196	9	2	6	1	6
3J2L_3	5S_rRNA links to Rfam database...	0.80	0.79	0.82	27	2987	10	0	6	4	7
3RKF_A	Purine links to Rfam database...	0.91	0.88	0.95	21	844	1	0	1	0	3
3SD1_A	THF links to Rfam database...	0.68	0.69	0.69	20	1504	9	4	5	0	9
3ZEX_D	5S_rRNA links to Rfam database...	0.88	0.83	0.94	29	2765	8	0	2	6	6
4A1C_3	5S_rRNA links to Rfam database...	0.88	0.86	0.89	32	2727	6	0	4	2	5
4A1C_2	5_8S_rRNA links to Rfam database...	0.20	0.25	0.16	5	4485	33	9	17	7	15
4AOB_A	SAM links to Rfam database...	0.59	0.55	0.64	16	1412	10	3	6	1	13
4ENB_A	crcB links to Rfam database...	0.39	0.33	0.50	5	462	6	0	5	1	10
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...	0.13	0.13	0.17	3	1184	15	2	13	0	21

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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 TurboFold(20) - scored higher in this pairwise comparison

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

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

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

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

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