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 PPfold(20) - 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 PPfold(20) & NanoFolder [.zip] - may take several seconds...

Overview

Metric	PPfold(20)		NanoFolder
MCC	0.664	>	0.271
Average MCC ± 95% Confidence Intervals	0.625 ± 0.155	>	0.294 ± 0.128
Sensitivity	0.541	>	0.286
Positive Predictive Value	0.818	>	0.266
Total TP	269	>	142
Total TN	82038	>	81834
Total FP	79	<	428
Total FP CONTRA	0	<	51
Total FP INCONS	60	<	340
Total FP COMP	19	<	37
Total FN	228	<	355
P-value	1.70887622364e-08

Performance plots

Comparison of performance of PPfold(20) and NanoFolder. Positive Predictive Value (PPV) is plotted against sensitivity. Each dot represents a single test of each method. See tables below for raw data (individual counts for PPfold(20) and NanoFolder).
Average Matthews Correlation Coefficients (MCC) with 95% confidence intervals (CIs) were plotted for different RNA families, for which at least 3 members were present in the benchmarking dataset. 'n' denotes the number of MCCs used to calculate the average and CI. See tables below for raw data (individual counts for PPfold(20) and NanoFolder).
Comparison of average Matthews Correlation Coefficients (MCCs) for PPfold(20) and NanoFolder. The whiskers correspond to 95% confidence intervals (CIs). 'n' denotes the number of MCCs used to calculate average MCCs and CIs. See tables below for raw data (individual counts for PPfold(20) and NanoFolder).

Performance of PPfold(20) - scored higher in this pairwise comparison

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

Total Base Pair Counts
Total TP	269
Total TN	82038
Total FP	79
Total FP CONTRA	0
Total FP INCONS	60
Total FP COMP	19
Total FN	228

Total Scores
MCC	0.664
Average MCC ± 95% Confidence Intervals	0.625 ± 0.155
Sensitivity	0.541
Positive Predictive Value	0.818
Nr of predictions	13

2. Individual counts for PPfold(20) [ download as .csv ]

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
3J20_1	tRNA links to Rfam database...	0.96	0.91	1.00	21	2905	0	0	0	0	2
3J2L_3	5S_rRNA links to Rfam database...	0.78	0.62	0.97	33	7841	3	0	1	2	20
3J3D_C	tRNA links to Rfam database...	0.80	0.68	0.95	19	2755	1	0	1	0	9
3J3E_7	5S_rRNA links to Rfam database...	0.74	0.61	0.89	33	7103	4	0	4	0	21
3J3E_8	5_8S_rRNA links to Rfam database...	0.14	0.09	0.23	3	7490	13	0	10	3	30
3J3F_8	5_8S_rRNA links to Rfam database...	0.33	0.25	0.43	9	12225	18	0	12	6	27
3J3F_7	5S_rRNA links to Rfam database...	0.80	0.68	0.94	34	7224	3	0	2	1	16
3ZEX_D	5S_rRNA links to Rfam database...	0.81	0.71	0.92	35	6983	3	0	3	0	14
3ZND_W	tRNA links to Rfam database...	0.47	0.43	0.53	10	2984	11	0	9	2	13
4A1C_3	5S_rRNA links to Rfam database...	0.77	0.63	0.94	34	7104	2	0	2	0	20
4A1C_2	5_8S_rRNA links to Rfam database...	0.21	0.15	0.29	5	11764	16	0	12	4	28
4AOB_A	SAM links to Rfam database...	0.74	0.60	0.93	25	4344	3	0	2	1	17
4ENC_A	crcB links to Rfam database...	0.58	0.42	0.80	8	1316	2	0	2	0	11

Performance of NanoFolder - scored lower in this pairwise comparison

1. Total counts & total scores for NanoFolder

Total Base Pair Counts
Total TP	142
Total TN	81834
Total FP	428
Total FP CONTRA	51
Total FP INCONS	340
Total FP COMP	37
Total FN	355

Total Scores
MCC	0.271
Average MCC ± 95% Confidence Intervals	0.294 ± 0.128
Sensitivity	0.286
Positive Predictive Value	0.266
Nr of predictions	13

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
3J20_1	tRNA links to Rfam database...	0.41	0.48	0.37	11	2896	19	5	14	0	12
3J2L_3	5S_rRNA links to Rfam database...	0.11	0.11	0.12	6	7824	46	3	42	1	47
3J3D_C	tRNA links to Rfam database...	0.70	0.71	0.69	20	2746	9	2	7	0	8
3J3E_7	5S_rRNA links to Rfam database...	0.35	0.33	0.37	18	7091	31	1	30	0	36
3J3E_8	5_8S_rRNA links to Rfam database...	0.00	0.00	0.00	0	7466	47	6	31	10	33
3J3F_8	5_8S_rRNA links to Rfam database...	0.27	0.33	0.22	12	12192	54	9	33	12	24
3J3F_7	5S_rRNA links to Rfam database...	0.17	0.18	0.17	9	7208	43	3	40	0	41
3ZEX_D	5S_rRNA links to Rfam database...	0.26	0.27	0.27	13	6972	36	1	35	0	36
3ZND_W	tRNA links to Rfam database...	0.18	0.22	0.17	5	2973	29	6	19	4	18
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
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.