CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

Home

Methods

Datasets

Rankings

RNA 2D Atlas

Help

FAQ

Contact us

RSS feeds

Twitter

Overview

Metric	PETfold_pre2.0(20)		NanoFolder
MCC	0.823	>	0.322
Average MCC ± 95% Confidence Intervals	0.769 ± 0.147	>	0.334 ± 0.132
Sensitivity	0.816	>	0.414
Positive Predictive Value	0.833	>	0.264
Total TP	284	>	144
Total TN	33792	>	33588
Total FP	121	<	474
Total FP CONTRA	12	<	144
Total FP INCONS	45	<	257
Total FP COMP	64	<	73
Total FN	64	<	204
P-value	2.06323189071e-08

^top

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).
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).
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).
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).

^top

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	284
Total TN	33792
Total FP	121
Total FP CONTRA	12
Total FP INCONS	45
Total FP COMP	64
Total FN	64

Total Scores
MCC	0.823
Average MCC ± 95% Confidence Intervals	0.769 ± 0.147
Sensitivity	0.816
Positive Predictive Value	0.833
Nr of predictions	14

^top

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...	1.00	1.00	1.00	20	1092	1	0	0	1	0
3J2L_3	5S_rRNA links to Rfam database...	0.97	0.94	1.00	32	2988	4	0	0	4	2
3J3D_C	tRNA links to Rfam database...	0.87	0.89	0.85	17	948	3	3	0	0	2
3J3E_7	5S_rRNA links to Rfam database...	0.94	0.94	0.94	32	2707	7	0	2	5	2
3J3E_8	5_8S_rRNA links to Rfam database...	0.48	0.47	0.50	7	2728	11	2	5	4	8
3J3F_7	5S_rRNA links to Rfam database...	0.93	0.92	0.94	33	2899	6	0	2	4	3
3J3F_8	5_8S_rRNA links to Rfam database...	0.34	0.37	0.32	7	4739	24	5	10	9	12
3J3V_B	5S_rRNA links to Rfam database...	0.90	0.89	0.92	24	2630	11	0	2	9	3
3ZEX_D	5S_rRNA links to Rfam database...	0.93	0.91	0.94	32	2762	6	0	2	4	3
3ZND_W	tRNA links to Rfam database...	0.67	0.75	0.60	6	1181	15	0	4	11	2
4A1C_2	5_8S_rRNA links to Rfam database...	0.25	0.25	0.25	5	4496	25	2	13	10	15
4A1C_3	5S_rRNA links to Rfam database...	1.00	1.00	1.00	37	2726	1	0	0	1	0
4AOB_A	SAM links to Rfam database...	0.87	0.83	0.92	24	1411	4	0	2	2	5
4ENC_A	crcB links to Rfam database...	0.61	0.53	0.73	8	485	3	0	3	0	7

^top

Performance of NanoFolder - scored lower in this pairwise comparison

1. Total counts & total scores for NanoFolder

Total Base Pair Counts
Total TP	144
Total TN	33588
Total FP	474
Total FP CONTRA	144
Total FP INCONS	257
Total FP COMP	73
Total FN	204

Total Scores
MCC	0.322
Average MCC ± 95% Confidence Intervals	0.334 ± 0.132
Sensitivity	0.414
Positive Predictive Value	0.264
Nr of predictions	14

^top

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_7	5S_rRNA links to Rfam database...	0.20	0.25	0.18	9	2883	43	10	32	1	27
3J3F_8	5_8S_rRNA links to Rfam database...	0.30	0.47	0.19	9	4714	57	21	17	19	10
3J3V_B	5S_rRNA links to Rfam database...	0.28	0.37	0.23	10	2612	38	13	21	4	17
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_2	5_8S_rRNA links to Rfam database...	-0.01	0.00	0.00	0	4469	61	18	29	14	20
4A1C_3	5S_rRNA links to Rfam database...	0.58	0.68	0.51	25	2714	24	9	15	0	12
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

^top

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

Table of contents:

Overview

Performance plots

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

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

2. Individual counts for PETfold_pre2.0(20) [ download as .csv ]

Performance of NanoFolder - scored lower in this pairwise comparison

1. Total counts & total scores for NanoFolder

2. Individual counts for NanoFolder [ download as .csv ]