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 ContextFold - scored higher in this pairwise comparison

Total counts & total scores
Individual counts

Performance of Alterna - scored lower in this pairwise comparison

Total counts & total scores
Individual counts

Compile and download dataset for ContextFold & Alterna [.zip] - may take several seconds...

Overview

Metric	ContextFold		Alterna
MCC	0.690	>	0.601
Average MCC ± 95% Confidence Intervals	0.714 ± 0.193	>	0.664 ± 0.192
Sensitivity	0.587	>	0.537
Positive Predictive Value	0.819	>	0.684
Total TP	118	>	108
Total TN	13746	>	13732
Total FP	27	<	56
Total FP CONTRA	1	<	8
Total FP INCONS	25	<	42
Total FP COMP	1	<	6
Total FN	83	<	93
P-value	2.24270395587e-08

Performance plots

Performance of ContextFold - scored higher in this pairwise comparison

1. Total counts & total scores for ContextFold

Total Base Pair Counts
Total TP	118
Total TN	13746
Total FP	27
Total FP CONTRA	1
Total FP INCONS	25
Total FP COMP	1
Total FN	83

Total Scores
MCC	0.690
Average MCC ± 95% Confidence Intervals	0.714 ± 0.193
Sensitivity	0.587
Positive Predictive Value	0.819
Nr of predictions	14

2. Individual counts for ContextFold [ 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...	0.55	0.50	0.63	10	1524	6	0	6	0	10
2LDL_A	-	0.90	0.82	1.00	9	342	0	0	0	0	2
2LK3_A	-	0.89	0.80	1.00	8	268	0	0	0	0	2
3J0L_7	-	-0.01	0.00	0.00	0	1212	13	0	13	0	17
3J0L_8	-	0.93	0.88	1.00	7	183	0	0	0	0	1
3J0L_g	-	-0.01	0.00	0.00	0	462	3	1	2	0	4
3J0L_a	-	0.71	0.56	0.90	9	1118	1	0	1	0	7
3J0L_1	-	0.70	0.58	0.85	11	1212	3	0	2	1	8
3J16_L	tRNA links to Rfam database...	0.75	0.57	1.00	17	2758	0	0	0	0	13
3SN2_B	IRE_II links to Rfam database...	0.96	0.92	1.00	11	395	0	0	0	0	1
3TRZ_Z	-	0.91	0.83	1.00	5	205	0	0	0	0	1
3TS0_U	-	1.00	1.00	1.00	6	247	0	0	0	0	0
3TS2_V	-	1.00	1.00	1.00	5	271	0	0	0	0	0
3UZL_B	tRNA links to Rfam database...	0.72	0.54	0.95	20	3549	1	0	1	0	17

Performance of Alterna - scored lower in this pairwise comparison

1. Total counts & total scores for Alterna

Total Base Pair Counts
Total TP	108
Total TN	13732
Total FP	56
Total FP CONTRA	8
Total FP INCONS	42
Total FP COMP	6
Total FN	93

Total Scores
MCC	0.601
Average MCC ± 95% Confidence Intervals	0.664 ± 0.192
Sensitivity	0.537
Positive Predictive Value	0.684
Nr of predictions	14

2. Individual counts for Alterna [ 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...	0.46	0.40	0.53	8	1525	7	0	7	0	12
2LDL_A	-	0.90	0.82	1.00	9	342	1	0	0	1	2
2LK3_A	-	0.95	0.90	1.00	9	267	0	0	0	0	1
3J0L_7	-	0.26	0.24	0.31	4	1212	9	0	9	0	13
3J0L_8	-	0.93	0.88	1.00	7	183	0	0	0	0	1
3J0L_g	-	-0.01	0.00	0.00	0	456	9	4	5	0	4
3J0L_a	-	0.23	0.19	0.30	3	1118	7	1	6	0	13
3J0L_1	-	0.61	0.53	0.71	10	1211	6	0	4	2	9
3J16_L	tRNA links to Rfam database...	0.63	0.53	0.76	16	2754	5	1	4	0	14
3SN2_B	IRE_II links to Rfam database...	0.91	0.83	1.00	10	396	0	0	0	0	2
3TRZ_Z	-	0.91	0.83	1.00	5	205	2	0	0	2	1
3TS0_U	-	1.00	1.00	1.00	6	247	1	0	0	1	0
3TS2_V	-	1.00	1.00	1.00	5	271	0	0	0	0	0
3UZL_B	tRNA links to Rfam database...	0.52	0.43	0.64	16	3545	9	2	7	0	21

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