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 CentroidHomfold‑LAST - scored higher in this pairwise comparison

Total counts & total scores
Individual counts

Performance of Mastr(20) - scored lower in this pairwise comparison

Total counts & total scores
Individual counts

Compile and download dataset for CentroidHomfold‑LAST & Mastr(20) [.zip] - may take several seconds...

Overview

Metric	CentroidHomfold‑LAST		Mastr(20)
MCC	0.654	>	0.592
Average MCC ± 95% Confidence Intervals	0.685 ± 0.163	>	0.549 ± 0.202
Sensitivity	0.524	>	0.417
Positive Predictive Value	0.822	<	0.846
Total TP	152	>	121
Total TN	35828	<	35870
Total FP	42	>	25
Total FP CONTRA	5	>	1
Total FP INCONS	28	>	21
Total FP COMP	9	>	3
Total FN	138	<	169
P-value	0.0

Performance plots

Performance of CentroidHomfold‑LAST - scored higher in this pairwise comparison

1. Total counts & total scores for CentroidHomfold‑LAST

Total Base Pair Counts
Total TP	152
Total TN	35828
Total FP	42
Total FP CONTRA	5
Total FP INCONS	28
Total FP COMP	9
Total FN	138

Total Scores
MCC	0.654
Average MCC ± 95% Confidence Intervals	0.685 ± 0.163
Sensitivity	0.524
Positive Predictive Value	0.822
Nr of predictions	9

2. Individual counts for CentroidHomfold‑LAST [ 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...	0.82	0.70	0.95	19	2983	3	0	1	2	8
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...	0.64	0.45	0.90	19	3895	2	0	2	0	23
4A1C_2	5_8S_rRNA links to Rfam database...	0.16	0.15	0.18	5	11753	29	5	18	6	28
4A1C_3	5S_rRNA links to Rfam database...	0.68	0.56	0.83	30	7104	6	0	6	0	24
4AOB_A	SAM links to Rfam database...	0.71	0.50	1.00	21	4350	1	0	0	1	21
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...	0.76	0.58	1.00	11	1315	0	0	0	0	8

Performance of Mastr(20) - scored lower in this pairwise comparison

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

Total Base Pair Counts
Total TP	121
Total TN	35870
Total FP	25
Total FP CONTRA	1
Total FP INCONS	21
Total FP COMP	3
Total FN	169

Total Scores
MCC	0.592
Average MCC ± 95% Confidence Intervals	0.549 ± 0.202
Sensitivity	0.417
Positive Predictive Value	0.846
Nr of predictions	9

2. Individual counts for Mastr(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...	0.87	0.80	0.94	16	973	1	0	1	0	4
3AMU_B	tRNA links to Rfam database...	0.77	0.59	1.00	16	2987	1	0	0	1	11
3RKF_A	Purine links to Rfam database...	0.70	0.50	1.00	17	2194	0	0	0	0	17
3SD1_A	THF links to Rfam database...	0.61	0.50	0.75	21	3888	7	1	6	0	21
4A1C_2	5_8S_rRNA links to Rfam database...	0.00	0.00	0.00	0	11781	0	0	0	0	33
4A1C_3	5S_rRNA links to Rfam database...	0.70	0.59	0.84	32	7102	7	0	6	1	22
4AOB_A	SAM links to Rfam database...	0.39	0.26	0.58	11	4352	9	0	8	1	31
4ENB_A	crcB links to Rfam database...	0.39	0.16	1.00	3	1272	0	0	0	0	16
4ENC_A	crcB links to Rfam database...	0.51	0.26	1.00	5	1321	0	0	0	0	14

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