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

Overview

Metric	RNASLOpt		TurboFold(seed)
MCC	0.467	>	0.460
Average MCC ± 95% Confidence Intervals	0.506 ± 0.235	>	0.454 ± 0.321
Sensitivity	0.380	=	0.380
Positive Predictive Value	0.582	>	0.563
Total TP	71	=	71
Total TN	27311	>	27307
Total FP	57	<	65
Total FP CONTRA	11	>	7
Total FP INCONS	40	<	48
Total FP COMP	6	<	10
Total FN	116	=	116
P-value	0.0

Performance plots

Performance of RNASLOpt - scored higher in this pairwise comparison

1. Total counts & total scores for RNASLOpt

Total Base Pair Counts
Total TP	71
Total TN	27311
Total FP	57
Total FP CONTRA	11
Total FP INCONS	40
Total FP COMP	6
Total FN	116

Total Scores
MCC	0.467
Average MCC ± 95% Confidence Intervals	0.506 ± 0.235
Sensitivity	0.380
Positive Predictive Value	0.582
Nr of predictions	6

2. Individual counts for RNASLOpt [ 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...	0.47	0.35	0.64	7	1529	4	0	4	0	13
4A1C_2	5_8S_rRNA links to Rfam database...	0.23	0.24	0.22	8	11744	35	8	21	6	25
4A1C_3	5S_rRNA links to Rfam database...	0.67	0.52	0.88	28	7108	4	0	4	0	26
4AOB_A	SAM links to Rfam database...	0.26	0.19	0.38	8	4350	13	2	11	0	34
4ENB_A	crcB links to Rfam database...	0.76	0.58	1.00	11	1264	0	0	0	0	8
4ENC_A	crcB links to Rfam database...	0.65	0.47	0.90	9	1316	1	1	0	0	10

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

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

Total Base Pair Counts
Total TP	71
Total TN	27307
Total FP	65
Total FP CONTRA	7
Total FP INCONS	48
Total FP COMP	10
Total FN	116

Total Scores
MCC	0.460
Average MCC ± 95% Confidence Intervals	0.454 ± 0.321
Sensitivity	0.380
Positive Predictive Value	0.563
Nr of predictions	6

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
2LC8_A	GP_knot1 links to Rfam database...	-0.01	0.00	0.00	0	1525	15	2	13	0	20
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.