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 ProbKnot - scored lower in this pairwise comparison

Total counts & total scores
Individual counts

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

Overview

Metric	TurboFold(20)		ProbKnot
MCC	0.620	>	0.574
Average MCC ± 95% Confidence Intervals	0.638 ± 0.156	>	0.605 ± 0.182
Sensitivity	0.500	<	0.514
Positive Predictive Value	0.775	>	0.648
Total TP	145	<	149
Total TN	35826	>	35783
Total FP	54	<	96
Total FP CONTRA	3	<	15
Total FP INCONS	39	<	66
Total FP COMP	12	<	15
Total FN	145	>	141
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 ProbKnot - scored lower in this pairwise comparison

1. Total counts & total scores for ProbKnot

Total Base Pair Counts
Total TP	149
Total TN	35783
Total FP	96
Total FP CONTRA	15
Total FP INCONS	66
Total FP COMP	15
Total FN	141

Total Scores
MCC	0.574
Average MCC ± 95% Confidence Intervals	0.605 ± 0.182
Sensitivity	0.514
Positive Predictive Value	0.648
Nr of predictions	9

2. Individual counts for ProbKnot [ 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...	0.65	0.59	0.73	16	2981	8	0	6	2	11
3RKF_A	Purine links to Rfam database...	0.73	0.59	0.91	20	2189	2	1	1	0	14
3SD1_A	THF links to Rfam database...	0.55	0.48	0.65	20	3885	11	2	9	0	22
4A1C_2	5_8S_rRNA links to Rfam database...	0.13	0.15	0.12	5	11738	49	7	31	11	28
4A1C_3	5S_rRNA links to Rfam database...	0.73	0.61	0.87	33	7102	6	1	4	1	21
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...	0.73	0.58	0.92	11	1263	1	1	0	0	8
4ENC_A	crcB links to Rfam database...	0.45	0.42	0.50	8	1310	8	1	7	0	11

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