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 TurboFold(20) - scored higher in this pairwise comparison

Total counts & total scores
Individual counts

Performance of Fold - scored lower in this pairwise comparison

Total counts & total scores
Individual counts

Compile and download dataset for TurboFold(20) & Fold [.zip] - may take several seconds...

Overview

Metric	TurboFold(20)		Fold
MCC	0.620	>	0.546
Average MCC ± 95% Confidence Intervals	0.638 ± 0.156	>	0.545 ± 0.198
Sensitivity	0.500	>	0.476
Positive Predictive Value	0.775	>	0.633
Total TP	145	>	138
Total TN	35826	>	35795
Total FP	54	<	94
Total FP CONTRA	3	<	11
Total FP INCONS	39	<	69
Total FP COMP	12	<	14
Total FN	145	<	152
P-value	0.0

Performance plots

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

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

Total Base Pair Counts
Total TP	145
Total TN	35826
Total FP	54
Total FP CONTRA	3
Total FP INCONS	39
Total FP COMP	12
Total FN	145

Total Scores
MCC	0.620
Average MCC ± 95% Confidence Intervals	0.638 ± 0.156
Sensitivity	0.500
Positive Predictive Value	0.775
Nr of predictions	9

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...	0.92	0.90	0.95	18	971	1	0	1	0	2
3AMU_B	tRNA links to Rfam database...	0.70	0.59	0.84	16	2984	5	0	3	2	11
3RKF_A	Purine links to Rfam database...	0.76	0.59	1.00	20	2191	0	0	0	0	14
3SD1_A	THF links to Rfam database...	0.59	0.48	0.74	20	3889	7	1	6	0	22
4A1C_2	5_8S_rRNA links to Rfam database...	0.18	0.15	0.21	5	11757	28	0	19	9	28
4A1C_3	5S_rRNA links to Rfam database...	0.69	0.57	0.84	31	7103	6	0	6	0	23
4AOB_A	SAM links to Rfam database...	0.56	0.40	0.77	17	4349	6	1	4	1	25
4ENB_A	crcB links to Rfam database...	0.69	0.47	1.00	9	1266	0	0	0	0	10
4ENC_A	crcB links to Rfam database...	0.65	0.47	0.90	9	1316	1	1	0	0	10

Performance of Fold - scored lower in this pairwise comparison

1. Total counts & total scores for Fold

Total Base Pair Counts
Total TP	138
Total TN	35795
Total FP	94
Total FP CONTRA	11
Total FP INCONS	69
Total FP COMP	14
Total FN	152

Total Scores
MCC	0.546
Average MCC ± 95% Confidence Intervals	0.545 ± 0.198
Sensitivity	0.476
Positive Predictive Value	0.633
Nr of predictions	9

2. Individual counts for Fold [ 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...	0.97	0.95	1.00	19	971	0	0	0	0	1
3AMU_B	tRNA links to Rfam database...	0.64	0.59	0.70	16	2980	9	0	7	2	11
3RKF_A	Purine links to Rfam database...	0.76	0.59	1.00	20	2191	0	0	0	0	14
3SD1_A	THF links to Rfam database...	0.57	0.48	0.69	20	3887	9	1	8	0	22
4A1C_2	5_8S_rRNA links to Rfam database...	0.14	0.15	0.14	5	11744	43	5	27	11	28
4A1C_3	5S_rRNA links to Rfam database...	0.68	0.57	0.82	31	7102	7	1	6	0	23
4AOB_A	SAM links to Rfam database...	0.50	0.40	0.63	17	4344	11	2	8	1	25
4ENB_A	crcB links to Rfam database...	0.32	0.26	0.42	5	1263	7	1	6	0	14
4ENC_A	crcB links to Rfam database...	0.31	0.26	0.38	5	1313	8	1	7	0	14

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