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 Alterna - scored higher in this pairwise comparison

Total counts & total scores
Individual counts

Performance of RNASLOpt - scored lower in this pairwise comparison

Total counts & total scores
Individual counts

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

Overview

Metric	Alterna		RNASLOpt
MCC	0.601	>	0.567
Average MCC ± 95% Confidence Intervals	0.664 ± 0.192	>	0.627 ± 0.206
Sensitivity	0.537	>	0.458
Positive Predictive Value	0.684	<	0.713
Total TP	108	>	92
Total TN	13732	<	13761
Total FP	56	>	43
Total FP CONTRA	8	>	2
Total FP INCONS	42	>	35
Total FP COMP	6	=	6
Total FN	93	<	109
P-value	2.57237423209e-08

Performance plots

Performance of Alterna - scored higher 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

Performance of RNASLOpt - scored lower in this pairwise comparison

1. Total counts & total scores for RNASLOpt

Total Base Pair Counts
Total TP	92
Total TN	13761
Total FP	43
Total FP CONTRA	2
Total FP INCONS	35
Total FP COMP	6
Total FN	109

Total Scores
MCC	0.567
Average MCC ± 95% Confidence Intervals	0.627 ± 0.206
Sensitivity	0.458
Positive Predictive Value	0.713
Nr of predictions	14

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
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	-	-0.01	0.00	0.00	0	1212	13	0	13	0	17
3J0L_8	-	0.70	0.50	1.00	4	186	0	0	0	0	4
3J0L_g	-	-0.01	0.00	0.00	0	461	4	1	3	0	4
3J0L_a	-	0.26	0.19	0.38	3	1120	5	1	4	0	13
3J0L_1	-	0.65	0.47	0.90	9	1215	3	0	1	2	10
3J16_L	tRNA links to Rfam database...	0.53	0.40	0.71	12	2758	5	0	5	0	18
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	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...	0.48	0.32	0.71	12	3553	5	0	5	0	25

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