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 PETfold_pre2.0(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 PETfold_pre2.0(20) & NanoFolder [.zip] - may take several seconds...

Overview

Metric	PETfold_pre2.0(20)		NanoFolder
MCC	0.667	>	0.269
Average MCC ± 95% Confidence Intervals	0.636 ± 0.133	>	0.291 ± 0.118
Sensitivity	0.552	>	0.280
Positive Predictive Value	0.810	>	0.267
Total TP	306	>	155
Total TN	89010	>	88807
Total FP	99	<	463
Total FP CONTRA	3	<	52
Total FP INCONS	69	<	374
Total FP COMP	27	<	37
Total FN	248	<	399
P-value	2.54914456376e-08

Performance plots

Comparison of performance of PETfold_pre2.0(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 PETfold_pre2.0(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 PETfold_pre2.0(20) and NanoFolder).
Comparison of average Matthews Correlation Coefficients (MCCs) for PETfold_pre2.0(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 PETfold_pre2.0(20) and NanoFolder).

Performance of PETfold_pre2.0(20) - scored higher in this pairwise comparison

1. Total counts & total scores for PETfold_pre2.0(20)

Total Base Pair Counts
Total TP	306
Total TN	89010
Total FP	99
Total FP CONTRA	3
Total FP INCONS	69
Total FP COMP	27
Total FN	248

Total Scores
MCC	0.667
Average MCC ± 95% Confidence Intervals	0.636 ± 0.133
Sensitivity	0.552
Positive Predictive Value	0.810
Nr of predictions	14

2. Individual counts for PETfold_pre2.0(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	0.63	0.87	34	7101	5	1	4	0	20
3J3E_8	5_8S_rRNA links to Rfam database...	0.32	0.21	0.50	7	7489	11	0	7	4	26
3J3F_8	5_8S_rRNA links to Rfam database...	0.30	0.25	0.38	9	12222	22	0	15	7	27
3J3F_7	5S_rRNA links to Rfam database...	0.78	0.68	0.89	34	7222	5	1	3	1	16
3J3V_B	5S_rRNA links to Rfam database...	0.65	0.51	0.83	29	6986	6	1	5	0	28
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...	0.82	0.69	0.97	37	7102	1	0	1	0	17
4A1C_2	5_8S_rRNA links to Rfam database...	0.19	0.15	0.25	5	11761	25	0	15	10	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...	0.55	0.42	0.73	8	1315	3	0	3	0	11

Performance of NanoFolder - scored lower in this pairwise comparison

1. Total counts & total scores for NanoFolder

Total Base Pair Counts
Total TP	155
Total TN	88807
Total FP	463
Total FP CONTRA	52
Total FP INCONS	374
Total FP COMP	37
Total FN	399

Total Scores
MCC	0.269
Average MCC ± 95% Confidence Intervals	0.291 ± 0.118
Sensitivity	0.280
Positive Predictive Value	0.267
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
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
3J3V_B	5S_rRNA links to Rfam database...	0.24	0.23	0.27	13	6973	35	1	34	0	44
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.