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 CRWrnafold - scored higher in this pairwise comparison

Total counts & total scores
Individual counts

Performance of NanoFolder - scored lower in this pairwise comparison

Total counts & total scores
Individual counts

Compile and download dataset for CRWrnafold & NanoFolder [.zip] - may take several seconds...

Overview

Metric	CRWrnafold		NanoFolder
MCC	0.584	>	0.475
Average MCC ± 95% Confidence Intervals	0.671 ± 0.182	>	0.628 ± 0.183
Sensitivity	0.519	>	0.484
Positive Predictive Value	0.664	>	0.474
Total TP	178	>	166
Total TN	40041	>	39959
Total FP	103	<	195
Total FP CONTRA	12	<	28
Total FP INCONS	78	<	156
Total FP COMP	13	>	11
Total FN	165	<	177
P-value	1.70887622364e-08

Performance plots

Performance of CRWrnafold - scored higher in this pairwise comparison

1. Total counts & total scores for CRWrnafold

Total Base Pair Counts
Total TP	178
Total TN	40041
Total FP	103
Total FP CONTRA	12
Total FP INCONS	78
Total FP COMP	13
Total FN	165

Total Scores
MCC	0.584
Average MCC ± 95% Confidence Intervals	0.671 ± 0.182
Sensitivity	0.519
Positive Predictive Value	0.664
Nr of predictions	14

2. Individual counts for CRWrnafold [ 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
2LDL_A	-	0.85	0.73	1.00	8	343	1	0	0	1	3
2LI4_A	-	0.93	0.88	1.00	14	482	0	0	0	0	2
2LK3_A	-	0.95	0.90	1.00	9	267	0	0	0	0	1
2LKR_A	-	0.52	0.44	0.63	17	6078	12	2	8	2	22
2LQZ_A	-	0.85	0.82	0.90	9	341	1	1	0	0	2
3J16_L	tRNA links to Rfam database...	0.84	0.70	1.00	21	2754	0	0	0	0	9
3SN2_B	IRE_II links to Rfam database...	0.96	0.92	1.00	11	395	0	0	0	0	1
3U4M_B	-	0.38	0.32	0.46	12	3134	14	0	14	0	25
4A1C_3	5S_rRNA links to Rfam database...	0.70	0.59	0.84	32	7102	6	0	6	0	22
4A1C_2	5_8S_rRNA links to Rfam database...	0.13	0.15	0.13	5	11741	44	4	31	9	28
4A4U_A	-	1.00	1.00	1.00	9	222	0	0	0	0	0
4AOB_A	SAM links to Rfam database...	0.59	0.48	0.74	20	4344	8	2	5	1	22
4ENC_A	crcB links to Rfam database...	0.70	0.58	0.85	11	1313	2	1	1	0	8

Performance of NanoFolder - scored lower in this pairwise comparison

1. Total counts & total scores for NanoFolder

Total Base Pair Counts
Total TP	166
Total TN	39959
Total FP	195
Total FP CONTRA	28
Total FP INCONS	156
Total FP COMP	11
Total FN	177

Total Scores
MCC	0.475
Average MCC ± 95% Confidence Intervals	0.628 ± 0.183
Sensitivity	0.484
Positive Predictive Value	0.474
Nr of predictions	14

2. Individual counts for NanoFolder [ 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...	0.52	0.55	0.50	11	1518	11	0	11	0	9
2LDL_A	-	0.90	0.82	1.00	9	342	1	0	0	1	2
2LI4_A	-	0.93	0.88	1.00	14	482	0	0	0	0	2
2LK3_A	-	0.95	0.90	1.00	9	267	0	0	0	0	1
2LKR_A	-	0.29	0.33	0.25	13	6054	38	8	30	0	26
2LQZ_A	-	0.91	0.91	0.91	10	340	1	1	0	0	1
3J16_L	tRNA links to Rfam database...	0.36	0.37	0.37	11	2745	19	3	16	0	19
3SN2_B	IRE_II links to Rfam database...	0.96	0.92	1.00	11	395	0	0	0	0	1
3U4M_B	-	0.61	0.57	0.66	21	3128	11	1	10	0	16
4A1C_3	5S_rRNA links to Rfam database...	0.48	0.46	0.51	25	7091	24	2	22	0	29
4A1C_2	5_8S_rRNA links to Rfam database...	0.00	0.00	0.00	0	11728	61	12	41	8	33
4A4U_A	-	1.00	1.00	1.00	9	222	0	0	0	0	0
4AOB_A	SAM links to Rfam database...	0.33	0.29	0.39	12	4340	20	1	18	1	30
4ENC_A	crcB links to Rfam database...	0.57	0.58	0.58	11	1307	9	0	8	1	8

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