CompaRNA - on-line benchmarks of RNA structure prediction methods

CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

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Table of contents:

Overview

Performance Plots

Performance of Afold - scored higher in this pairwise comparison

Total counts & total scores
Individual counts

Performance of NanoFolder - scored lower in this pairwise comparison

Total counts & total scores
Individual counts

Compile and download dataset for Afold & NanoFolder [.zip] - may take several seconds...

Overview

Metric	Afold		NanoFolder
MCC	0.683	>	0.548
Average MCC ± 95% Confidence Intervals	0.781 ± 0.172	>	0.737 ± 0.204
Sensitivity	0.643	>	0.576
Positive Predictive Value	0.731	>	0.529
Total TP	144	>	129
Total TN	25626	>	25579
Total FP	71	<	125
Total FP CONTRA	6	<	22
Total FP INCONS	47	<	93
Total FP COMP	18	>	10
Total FN	80	<	95
P-value	2.22210847902e-08

Performance plots

Performance of Afold - scored higher in this pairwise comparison

1. Total counts & total scores for Afold

Total Base Pair Counts
Total TP	144
Total TN	25626
Total FP	71
Total FP CONTRA	6
Total FP INCONS	47
Total FP COMP	18
Total FN	80

Total Scores
MCC	0.683
Average MCC ± 95% Confidence Intervals	0.781 ± 0.172
Sensitivity	0.643
Positive Predictive Value	0.731
Nr of predictions	12

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

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2LC8_A	GP_knot1 links to Rfam database...	0.61	0.55	0.69	11	1524	6	0	5	1	9
2LDL_A	-	0.90	0.82	1.00	9	342	1	0	0	1	2
2LI4_A	-	0.93	0.88	1.00	14	482	0	0	0	0	2
2LK3_A	-	0.95	0.90	1.00	9	267	0	0	0	0	1
2LKR_A	-	0.93	0.87	1.00	34	6071	3	0	0	3	5
2LQZ_A	-	0.85	0.82	0.90	9	341	1	1	0	0	2
2LWK_A	-	0.75	0.69	0.82	9	485	2	0	2	0	4
3SN2_B	IRE_II links to Rfam database...	0.96	0.92	1.00	11	395	0	0	0	0	1
3U4M_B	-	0.38	0.32	0.46	12	3134	14	0	14	0	25
3VJR_D	-	0.96	0.92	1.00	12	618	1	0	0	1	1
4A1C_2	5_8S_rRNA links to Rfam database...	0.14	0.15	0.14	5	11745	43	5	26	12	28
4A4U_A	-	1.00	1.00	1.00	9	222	0	0	0	0	0

Performance of NanoFolder - scored lower in this pairwise comparison

1. Total counts & total scores for NanoFolder

Total Base Pair Counts
Total TP	129
Total TN	25579
Total FP	125
Total FP CONTRA	22
Total FP INCONS	93
Total FP COMP	10
Total FN	95

Total Scores
MCC	0.548
Average MCC ± 95% Confidence Intervals	0.737 ± 0.204
Sensitivity	0.576
Positive Predictive Value	0.529
Nr of predictions	12

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

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2LC8_A	GP_knot1 links to Rfam database...	0.52	0.55	0.50	11	1518	11	0	11	0	9
2LDL_A	-	0.90	0.82	1.00	9	342	1	0	0	1	2
2LI4_A	-	0.93	0.88	1.00	14	482	0	0	0	0	2
2LK3_A	-	0.95	0.90	1.00	9	267	0	0	0	0	1
2LKR_A	-	0.29	0.33	0.25	13	6054	38	8	30	0	26
2LQZ_A	-	0.91	0.91	0.91	10	340	1	1	0	0	1
2LWK_A	-	0.83	0.77	0.91	10	485	2	0	1	1	3
3SN2_B	IRE_II links to Rfam database...	0.96	0.92	1.00	11	395	0	0	0	0	1
3U4M_B	-	0.61	0.57	0.66	21	3128	11	1	10	0	16
3VJR_D	-	0.96	0.92	1.00	12	618	0	0	0	0	1
4A1C_2	5_8S_rRNA links to Rfam database...	0.00	0.00	0.00	0	11728	61	12	41	8	33
4A4U_A	-	1.00	1.00	1.00	9	222	0	0	0	0	0

Matthews Correlation Coeffient, Sensitivity and Positive Predictive Value have been calculated based on the paper by Gardener & Giegerich, 2004.