CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

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Overview

Metric	PETfold_pre2.0(seed)		CentroidHomfold‑LAST
MCC	0.729	>	0.574
Average MCC ± 95% Confidence Intervals	0.702 ± 0.065	>	0.567 ± 0.112
Sensitivity	0.606	>	0.489
Positive Predictive Value	0.882	>	0.680
Total TP	502	>	405
Total TN	117069	>	117042
Total FP	93	<	218
Total FP CONTRA	6	<	21
Total FP INCONS	61	<	170
Total FP COMP	26	<	27
Total FN	327	<	424
P-value	5.23657817852e-08

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Performance plots

Comparison of performance of PETfold_pre2.0(seed) and CentroidHomfold-LAST. 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(seed) and CentroidHomfold‑LAST).
Comparison of performance of PETfold_pre2.0(seed) and CentroidHomfold-LAST. 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(seed) and CentroidHomfold‑LAST).
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(seed) and CentroidHomfold‑LAST).
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(seed) and CentroidHomfold‑LAST).
Comparison of average Matthews Correlation Coefficients (MCCs) for PETfold_pre2.0(seed) and CentroidHomfold-LAST. 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(seed) and CentroidHomfold‑LAST).
Comparison of average Matthews Correlation Coefficients (MCCs) for PETfold_pre2.0(seed) and CentroidHomfold-LAST. 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(seed) and CentroidHomfold‑LAST).

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

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

Total Base Pair Counts
Total TP	502
Total TN	117069
Total FP	93
Total FP CONTRA	6
Total FP INCONS	61
Total FP COMP	26
Total FN	327

Total Scores
MCC	0.729
Average MCC ± 95% Confidence Intervals	0.702 ± 0.065
Sensitivity	0.606
Positive Predictive Value	0.882
Nr of predictions	23

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2. Individual counts for PETfold_pre2.0(seed) [ 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...	0.40	0.30	0.55	6	1529	5	0	5	0	14
3J16_L	tRNA links to Rfam database...	0.82	0.70	0.95	21	2753	1	0	1	0	9
3J20_0	tRNA links to Rfam database...	0.84	0.70	1.00	21	2829	1	0	0	1	9
3J20_1	tRNA links to Rfam database...	0.96	0.91	1.00	21	2905	1	0	0	1	2
3J2L_3	5S_rRNA links to Rfam database...	0.77	0.62	0.94	33	7840	4	0	2	2	20
3J3D_C	tRNA links to Rfam database...	0.82	0.71	0.95	20	2754	2	0	1	1	8
3J3E_7	5S_rRNA links to Rfam database...	0.78	0.67	0.92	36	7101	3	0	3	0	18
3J3E_8	5_8S_rRNA links to Rfam database...	0.43	0.30	0.63	10	7487	8	0	6	2	23
3J3F_7	5S_rRNA links to Rfam database...	0.85	0.74	0.97	37	7222	2	0	1	1	13
3J3F_8	5_8S_rRNA links to Rfam database...	0.63	0.53	0.76	19	12221	10	0	6	4	17
3J3V_B	5S_rRNA links to Rfam database...	0.76	0.61	0.95	35	6984	3	0	2	1	22
3UZL_B	tRNA links to Rfam database...	0.72	0.54	0.95	20	3549	2	1	0	1	17
3W3S_B	tRNA-Sec links to Rfam database...	0.78	0.65	0.93	26	4725	4	0	2	2	14
3ZEX_D	5S_rRNA links to Rfam database...	0.82	0.73	0.92	36	6982	3	0	3	0	13
3ZND_W	tRNA links to Rfam database...	0.47	0.43	0.53	10	2984	12	0	9	3	13
4A1C_2	5_8S_rRNA links to Rfam database...	0.57	0.45	0.71	15	11760	12	0	6	6	18
4A1C_3	5S_rRNA links to Rfam database...	0.83	0.70	0.97	38	7101	1	0	1	0	16
4AOB_A	SAM links to Rfam database...	0.72	0.57	0.92	24	4345	3	0	2	1	18
4ENB_A	crcB links to Rfam database...	0.50	0.42	0.62	8	1262	5	1	4	0	11
4ENC_A	crcB links to Rfam database...	0.50	0.42	0.62	8	1313	5	1	4	0	11
4FRG_B	AdoCbl-variant links to Rfam database...	0.74	0.63	0.87	20	3463	3	1	2	0	12
4FRN_A	AdoCbl-variant links to Rfam database...	0.73	0.61	0.88	22	5126	3	2	1	0	14
4JF2_A	preQ1-II links to Rfam database...	0.72	0.52	1.00	16	2834	0	0	0	0	15

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Performance of CentroidHomfold‑LAST - scored lower in this pairwise comparison

1. Total counts & total scores for CentroidHomfold‑LAST

Total Base Pair Counts
Total TP	405
Total TN	117042
Total FP	218
Total FP CONTRA	21
Total FP INCONS	170
Total FP COMP	27
Total FN	424

Total Scores
MCC	0.574
Average MCC ± 95% Confidence Intervals	0.567 ± 0.112
Sensitivity	0.489
Positive Predictive Value	0.680
Nr of predictions	23

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2. Individual counts for CentroidHomfold‑LAST [ 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...	-0.01	0.00	0.00	0	1529	11	0	11	0	20
3J16_L	tRNA links to Rfam database...	0.75	0.57	1.00	17	2758	0	0	0	0	13
3J20_0	tRNA links to Rfam database...	0.35	0.37	0.34	11	2818	22	3	18	1	19
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...	0.73	0.62	0.87	33	7837	7	0	5	2	20
3J3D_C	tRNA links to Rfam database...	0.68	0.61	0.77	17	2753	5	0	5	0	11
3J3E_7	5S_rRNA links to Rfam database...	0.64	0.54	0.76	29	7102	9	0	9	0	25
3J3E_8	5_8S_rRNA links to Rfam database...	0.05	0.03	0.08	1	7490	16	1	11	4	32
3J3F_7	5S_rRNA links to Rfam database...	0.65	0.58	0.74	29	7221	10	1	9	0	21
3J3F_8	5_8S_rRNA links to Rfam database...	0.33	0.33	0.33	12	12210	33	4	20	9	24
3J3V_B	5S_rRNA links to Rfam database...	0.51	0.37	0.72	21	6992	8	1	7	0	36
3UZL_B	tRNA links to Rfam database...	0.72	0.54	0.95	20	3549	1	0	1	0	17
3W3S_B	tRNA-Sec links to Rfam database...	0.85	0.73	1.00	29	4724	1	0	0	1	11
3ZEX_D	5S_rRNA links to Rfam database...	0.75	0.65	0.86	32	6984	5	0	5	0	17
3ZND_W	tRNA links to Rfam database...	0.47	0.39	0.56	9	2987	10	0	7	3	14
4A1C_2	5_8S_rRNA links to Rfam database...	0.16	0.15	0.18	5	11753	29	5	18	6	28
4A1C_3	5S_rRNA links to Rfam database...	0.68	0.56	0.83	30	7104	6	0	6	0	24
4AOB_A	SAM links to Rfam database...	0.71	0.50	1.00	21	4350	1	0	0	1	21
4ENB_A	crcB links to Rfam database...	0.76	0.58	1.00	11	1264	0	0	0	0	8
4ENC_A	crcB links to Rfam database...	0.76	0.58	1.00	11	1315	0	0	0	0	8
4FRG_B	AdoCbl-variant links to Rfam database...	0.41	0.41	0.43	13	3456	17	3	14	0	19
4FRN_A	AdoCbl-variant links to Rfam database...	0.36	0.39	0.34	14	5110	27	3	24	0	22
4JF2_A	preQ1-II links to Rfam database...	0.78	0.61	1.00	19	2831	0	0	0	0	12

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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(seed) - scored higher in this pairwise comparison

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

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

Performance of CentroidHomfold‑LAST - scored lower in this pairwise comparison

1. Total counts & total scores for CentroidHomfold‑LAST

2. Individual counts for CentroidHomfold‑LAST [ download as .csv ]