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 MXScarna(seed) - scored higher in this pairwise comparison

Total counts & total scores
Individual counts

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

Total counts & total scores
Individual counts

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

Overview

Metric	MXScarna(seed)		TurboFold(seed)
MCC	0.573	>	0.550
Average MCC ± 95% Confidence Intervals	0.510 ± 0.182	<	0.555 ± 0.229
Sensitivity	0.459	>	0.456
Positive Predictive Value	0.722	>	0.672
Total TP	130	>	129
Total TN	34370	>	34358
Total FP	65	<	73
Total FP CONTRA	4	<	8
Total FP INCONS	46	<	55
Total FP COMP	15	>	10
Total FN	153	<	154
P-value	0.0

Performance plots

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

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

Total Base Pair Counts
Total TP	130
Total TN	34370
Total FP	65
Total FP CONTRA	4
Total FP INCONS	46
Total FP COMP	15
Total FN	153

Total Scores
MCC	0.573
Average MCC ± 95% Confidence Intervals	0.510 ± 0.182
Sensitivity	0.459
Positive Predictive Value	0.722
Nr of predictions	9

2. Individual counts for MXScarna(seed) [ 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...	0.57	0.55	0.61	11	972	7	0	7	0	9
2LC8_A	GP_knot1 links to Rfam database...	-0.01	0.00	0.00	0	1530	12	0	10	2	20
3RKF_A	Purine links to Rfam database...	0.72	0.53	1.00	18	2193	0	0	0	0	16
3SD1_A	THF links to Rfam database...	0.63	0.55	0.74	23	3885	8	1	7	0	19
4A1C_2	5_8S_rRNA links to Rfam database...	0.35	0.24	0.50	8	11765	20	1	7	12	25
4A1C_3	5S_rRNA links to Rfam database...	0.75	0.65	0.88	35	7100	5	1	4	0	19
4AOB_A	SAM links to Rfam database...	0.66	0.55	0.79	23	4342	7	0	6	1	19
4ENB_A	crcB links to Rfam database...	0.48	0.32	0.75	6	1267	2	0	2	0	13
4ENC_A	crcB links to Rfam database...	0.43	0.32	0.60	6	1316	4	1	3	0	13

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

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

Total Base Pair Counts
Total TP	129
Total TN	34358
Total FP	73
Total FP CONTRA	8
Total FP INCONS	55
Total FP COMP	10
Total FN	154

Total Scores
MCC	0.550
Average MCC ± 95% Confidence Intervals	0.555 ± 0.229
Sensitivity	0.456
Positive Predictive Value	0.672
Nr of predictions	9

2. Individual counts for TurboFold(seed) [ 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
2LC8_A	GP_knot1 links to Rfam database...	-0.01	0.00	0.00	0	1525	15	2	13	0	20
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...	0.15	0.15	0.15	5	11748	37	3	25	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

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