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(seed) - 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(seed) & ProbKnot [.zip] - may take several seconds...

Overview

Metric	TurboFold(seed)		ProbKnot
MCC	0.550	>	0.526
Average MCC ± 95% Confidence Intervals	0.555 ± 0.229	>	0.531 ± 0.239
Sensitivity	0.456	<	0.470
Positive Predictive Value	0.672	>	0.596
Total TP	129	<	133
Total TN	34358	>	34327
Total FP	73	<	103
Total FP CONTRA	8	<	17
Total FP INCONS	55	<	73
Total FP COMP	10	<	13
Total FN	154	>	150
P-value	0.0

Performance plots

Performance of TurboFold(seed) - scored higher 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

Performance of ProbKnot - scored lower in this pairwise comparison

1. Total counts & total scores for ProbKnot

Total Base Pair Counts
Total TP	133
Total TN	34327
Total FP	103
Total FP CONTRA	17
Total FP INCONS	73
Total FP COMP	13
Total FN	150

Total Scores
MCC	0.526
Average MCC ± 95% Confidence Intervals	0.531 ± 0.239
Sensitivity	0.470
Positive Predictive Value	0.596
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
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...	0.73	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.