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

Overview

Metric	RSpredict(20)		NanoFolder
MCC	0.618	>	0.326
Average MCC ± 95% Confidence Intervals	0.569 ± 0.167	>	0.338 ± 0.143
Sensitivity	0.573	>	0.417
Positive Predictive Value	0.674	>	0.267
Total TP	184	>	134
Total TN	31204	>	30976
Total FP	129	<	436
Total FP CONTRA	31	<	131
Total FP INCONS	58	<	236
Total FP COMP	40	<	69
Total FN	137	<	187
P-value	2.18141491686e-08

Performance plots

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

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

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

Total Base Pair Counts
Total TP	184
Total TN	31204
Total FP	129
Total FP CONTRA	31
Total FP INCONS	58
Total FP COMP	40
Total FN	137

Total Scores
MCC	0.618
Average MCC ± 95% Confidence Intervals	0.569 ± 0.167
Sensitivity	0.573
Positive Predictive Value	0.674
Nr of predictions	13

2. Individual counts for RSpredict(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...	0.67	0.50	0.91	10	1101	2	0	1	1	10
3J2L_3	5S_rRNA links to Rfam database...	0.71	0.59	0.87	20	2997	6	0	3	3	14
3J3D_C	tRNA links to Rfam database...	0.82	0.84	0.80	16	948	4	3	1	0	3
3J3E_7	5S_rRNA links to Rfam database...	0.82	0.79	0.84	27	2709	7	0	5	2	7
3J3E_8	5_8S_rRNA links to Rfam database...	-0.01	0.00	0.00	0	2724	19	5	13	1	15
3J3F_8	5_8S_rRNA links to Rfam database...	0.42	0.47	0.38	9	4737	26	9	6	11	10
3J3F_7	5S_rRNA links to Rfam database...	0.94	0.94	0.94	34	2898	3	1	1	1	2
3ZEX_D	5S_rRNA links to Rfam database...	0.88	0.83	0.94	29	2765	7	0	2	5	6
3ZND_W	tRNA links to Rfam database...	0.47	0.38	0.60	3	1186	9	0	2	7	5
4A1C_3	5S_rRNA links to Rfam database...	0.60	0.49	0.75	18	2739	8	0	6	2	19
4A1C_2	5_8S_rRNA links to Rfam database...	0.25	0.30	0.21	6	4487	30	12	11	7	14
4AOB_A	SAM links to Rfam database...	0.33	0.21	0.55	6	1426	5	1	4	0	23
4ENC_A	crcB links to Rfam database...	0.51	0.40	0.67	6	487	3	0	3	0	9

Performance of NanoFolder - scored lower in this pairwise comparison

1. Total counts & total scores for NanoFolder

Total Base Pair Counts
Total TP	134
Total TN	30976
Total FP	436
Total FP CONTRA	131
Total FP INCONS	236
Total FP COMP	69
Total FN	187

Total Scores
MCC	0.326
Average MCC ± 95% Confidence Intervals	0.338 ± 0.143
Sensitivity	0.417
Positive Predictive Value	0.267
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...	0.42	0.50	0.37	10	1085	20	5	12	3	10
3J2L_3	5S_rRNA links to Rfam database...	0.13	0.18	0.12	6	2969	46	14	31	1	28
3J3D_C	tRNA links to Rfam database...	0.76	0.95	0.62	18	939	11	9	2	0	1
3J3E_7	5S_rRNA links to Rfam database...	0.44	0.53	0.38	18	2693	31	10	20	1	16
3J3E_8	5_8S_rRNA links to Rfam database...	-0.01	0.00	0.00	0	2707	47	11	24	12	15
3J3F_8	5_8S_rRNA links to Rfam database...	0.30	0.47	0.19	9	4714	57	21	17	19	10
3J3F_7	5S_rRNA links to Rfam database...	0.20	0.25	0.18	9	2883	43	10	32	1	27
3ZEX_D	5S_rRNA links to Rfam database...	0.30	0.37	0.27	13	2747	36	10	26	0	22
3ZND_W	tRNA links to Rfam database...	0.24	0.38	0.16	3	1172	31	8	8	15	5
4A1C_3	5S_rRNA links to Rfam database...	0.58	0.68	0.51	25	2714	24	9	15	0	12
4A1C_2	5_8S_rRNA links to Rfam database...	-0.01	0.00	0.00	0	4469	61	18	29	14	20
4AOB_A	SAM links to Rfam database...	0.39	0.41	0.39	12	1406	20	4	15	1	17
4ENC_A	crcB links to Rfam database...	0.66	0.73	0.61	11	478	9	2	5	2	4

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