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 Afold - 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 Afold & RNASLOpt [.zip] - may take several seconds...

Overview

Metric	Afold		RNASLOpt
MCC	0.677	>	0.646
Average MCC ± 95% Confidence Intervals	0.748 ± 0.148	>	0.733 ± 0.146
Sensitivity	0.624	>	0.572
Positive Predictive Value	0.740	>	0.736
Total TP	216	>	198
Total TN	36378	<	36401
Total FP	99	>	83
Total FP CONTRA	8	<	9
Total FP INCONS	68	>	62
Total FP COMP	23	>	12
Total FN	130	<	148
P-value	2.50323628132e-08

Performance plots

Performance of Afold - scored higher in this pairwise comparison

1. Total counts & total scores for Afold

Total Base Pair Counts
Total TP	216
Total TN	36378
Total FP	99
Total FP CONTRA	8
Total FP INCONS	68
Total FP COMP	23
Total FN	130

Total Scores
MCC	0.677
Average MCC ± 95% Confidence Intervals	0.748 ± 0.148
Sensitivity	0.624
Positive Predictive Value	0.740
Nr of predictions	18

2. Individual counts for Afold [ 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...	0.61	0.55	0.69	11	1524	6	0	5	1	9
2LDL_A	-	0.90	0.82	1.00	9	342	1	0	0	1	2
2LHP_A	-	0.97	0.94	1.00	15	651	0	0	0	0	1
2LI4_A	-	0.93	0.88	1.00	14	482	0	0	0	0	2
2LJJ_A	-	1.00	1.00	1.00	8	343	2	0	0	2	0
2LK3_A	-	0.95	0.90	1.00	9	267	0	0	0	0	1
2LKR_A	-	0.93	0.87	1.00	34	6071	3	0	0	3	5
2LQZ_A	-	0.85	0.82	0.90	9	341	1	1	0	0	2
2LWK_A	-	0.75	0.69	0.82	9	485	2	0	2	0	4
3J0L_1	-	0.73	0.63	0.86	12	1211	3	0	2	1	7
3J0L_h	-	0.73	0.60	0.90	26	6076	5	0	3	2	17
3J0L_7	-	-0.01	0.00	0.00	0	1210	15	1	14	0	17
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
3VJR_D	-	0.96	0.92	1.00	12	618	1	0	0	1	1
4A1C_2	5_8S_rRNA links to Rfam database...	0.14	0.15	0.14	5	11745	43	5	26	12	28
4A4U_A	-	1.00	1.00	1.00	9	222	0	0	0	0	0
4ENB_A	crcB links to Rfam database...	0.67	0.58	0.79	11	1261	3	1	2	0	8

Performance of RNASLOpt - scored lower in this pairwise comparison

1. Total counts & total scores for RNASLOpt

Total Base Pair Counts
Total TP	198
Total TN	36401
Total FP	83
Total FP CONTRA	9
Total FP INCONS	62
Total FP COMP	12
Total FN	148

Total Scores
MCC	0.646
Average MCC ± 95% Confidence Intervals	0.733 ± 0.146
Sensitivity	0.572
Positive Predictive Value	0.736
Nr of predictions	18

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
2LHP_A	-	0.97	0.94	1.00	15	651	0	0	0	0	1
2LI4_A	-	0.93	0.88	1.00	14	482	0	0	0	0	2
2LJJ_A	-	1.00	1.00	1.00	8	343	2	0	0	2	0
2LK3_A	-	0.95	0.90	1.00	9	267	0	0	0	0	1
2LKR_A	-	0.68	0.62	0.75	24	6073	9	0	8	1	15
2LQZ_A	-	0.85	0.82	0.90	9	341	1	1	0	0	2
2LWK_A	-	0.83	0.77	0.91	10	485	1	0	1	0	3
3J0L_1	-	0.65	0.47	0.90	9	1215	3	0	1	2	10
3J0L_h	-	0.70	0.49	1.00	21	6084	0	0	0	0	22
3J0L_7	-	-0.01	0.00	0.00	0	1212	13	0	13	0	17
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
3VJR_D	-	0.96	0.92	1.00	12	618	0	0	0	0	1
4A1C_2	5_8S_rRNA links to Rfam database...	0.23	0.24	0.22	8	11744	35	8	21	6	25
4A4U_A	-	1.00	1.00	1.00	9	222	0	0	0	0	0
4ENB_A	crcB links to Rfam database...	0.76	0.58	1.00	11	1264	0	0	0	0	8

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