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)		PPfold(seed)
MCC	0.865	>	0.166
Average MCC ± 95% Confidence Intervals	0.833 ± 0.064	>	0.070 ± 0.077
Sensitivity	0.823	>	0.045
Positive Predictive Value	0.912	>	0.634
Total TP	478	>	26
Total TN	48797	<	49280
Total FP	137	>	80
Total FP CONTRA	17	>	1
Total FP INCONS	29	>	14
Total FP COMP	91	>	65
Total FN	103	<	555
P-value	5.1503931209e-08

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Performance plots

Comparison of performance of PETfold_pre2.0(seed) and PPfold(seed). 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 PPfold(seed)).
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 PPfold(seed)).
Comparison of average Matthews Correlation Coefficients (MCCs) for PETfold_pre2.0(seed) and PPfold(seed). 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 PPfold(seed)).

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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	478
Total TN	48797
Total FP	137
Total FP CONTRA	17
Total FP INCONS	29
Total FP COMP	91
Total FN	103

Total Scores
MCC	0.865
Average MCC ± 95% Confidence Intervals	0.833 ± 0.064
Sensitivity	0.823
Positive Predictive Value	0.912
Nr of predictions	24

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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...	0.41	0.33	0.55	6	517	5	0	5	0	12
3J16_L	tRNA links to Rfam database...	1.00	1.00	1.00	21	1138	1	0	0	1	0
3J20_1	tRNA links to Rfam database...	1.00	1.00	1.00	20	1092	2	0	0	2	0
3J20_0	tRNA links to Rfam database...	0.95	0.95	0.95	20	1198	2	1	0	1	1
3J2L_3	5S_rRNA links to Rfam database...	0.97	0.94	1.00	32	2988	5	0	0	5	2
3J3D_C	tRNA links to Rfam database...	0.90	0.95	0.86	18	947	4	3	0	1	1
3J3E_7	5S_rRNA links to Rfam database...	0.97	0.97	0.97	33	2707	6	0	1	5	1
3J3E_8	5_8S_rRNA links to Rfam database...	0.71	0.67	0.77	10	2729	8	1	2	5	5
3J3F_7	5S_rRNA links to Rfam database...	0.99	0.97	1.00	35	2899	4	0	0	4	1
3J3F_8	5_8S_rRNA links to Rfam database...	0.86	0.84	0.89	16	4743	13	2	0	11	3
3UZL_B	tRNA links to Rfam database...	0.93	0.88	1.00	14	1279	8	0	0	8	2
3W1K_J	tRNA-Sec links to Rfam database...	0.85	0.81	0.89	25	1650	4	2	1	1	6
3W3S_B	tRNA-Sec links to Rfam database...	0.80	0.73	0.89	24	1962	6	1	2	3	9
3ZEX_D	5S_rRNA links to Rfam database...	0.96	0.94	0.97	33	2762	6	0	1	5	2
3ZEX_C	5_8S_rRNA links to Rfam database...	0.70	0.59	0.85	17	5354	12	1	2	9	12
3ZND_W	tRNA links to Rfam database...	0.67	0.75	0.60	6	1181	16	0	4	12	2
4A1C_3	5S_rRNA links to Rfam database...	1.00	1.00	1.00	37	2726	2	0	0	2	0
4A1C_2	5_8S_rRNA links to Rfam database...	0.79	0.75	0.83	15	4498	12	1	2	9	5
4AOB_A	SAM links to Rfam database...	0.85	0.79	0.92	23	1412	4	0	2	2	6
4ENB_A	crcB links to Rfam database...	0.61	0.53	0.73	8	461	5	1	2	2	7
4ENC_A	crcB links to Rfam database...	0.61	0.53	0.73	8	485	5	1	2	2	7
4FRG_B	AdoCbl-variant links to Rfam database...	0.87	0.83	0.91	20	1180	3	0	2	1	4
4FRN_A	AdoCbl-variant links to Rfam database...	0.83	0.79	0.88	22	1823	3	2	1	0	6
4JF2_A	preQ1-II links to Rfam database...	0.76	0.63	0.94	15	1066	1	1	0	0	9

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Performance of PPfold(seed) - scored lower in this pairwise comparison

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

Total Base Pair Counts
Total TP	26
Total TN	49280
Total FP	80
Total FP CONTRA	1
Total FP INCONS	14
Total FP COMP	65
Total FN	555

Total Scores
MCC	0.166
Average MCC ± 95% Confidence Intervals	0.070 ± 0.077
Sensitivity	0.045
Positive Predictive Value	0.634
Nr of predictions	24

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2. Individual counts for PPfold(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...	0.49	0.33	0.75	6	520	2	0	2	0	12
3J16_L	tRNA links to Rfam database...	0.00	0.00	0.00	0	1159	0	0	0	0	21
3J20_1	tRNA links to Rfam database...	0.00	0.00	0.00	0	1112	0	0	0	0	20
3J20_0	tRNA links to Rfam database...	0.00	0.00	0.00	0	1219	0	0	0	0	21
3J2L_3	5S_rRNA links to Rfam database...	0.00	0.00	0.00	0	3020	0	0	0	0	34
3J3D_C	tRNA links to Rfam database...	0.00	0.00	0.00	0	968	0	0	0	0	19
3J3E_7	5S_rRNA links to Rfam database...	0.00	0.00	0.00	0	2741	0	0	0	0	34
3J3E_8	5_8S_rRNA links to Rfam database...	0.00	0.00	0.00	0	2742	6	0	0	6	15
3J3F_7	5S_rRNA links to Rfam database...	0.00	0.00	0.00	0	2934	0	0	0	0	36
3J3F_8	5_8S_rRNA links to Rfam database...	0.19	0.11	0.33	2	4755	24	0	4	20	17
3UZL_B	tRNA links to Rfam database...	0.00	0.00	0.00	0	1293	0	0	0	0	16
3W1K_J	tRNA-Sec links to Rfam database...	0.00	0.00	0.00	0	1678	0	0	0	0	31
3W3S_B	tRNA-Sec links to Rfam database...	0.00	0.00	0.00	0	1989	0	0	0	0	33
3ZEX_D	5S_rRNA links to Rfam database...	0.00	0.00	0.00	0	2796	0	0	0	0	35
3ZEX_C	5_8S_rRNA links to Rfam database...	0.15	0.07	0.33	2	5368	24	0	4	20	27
3ZND_W	tRNA links to Rfam database...	0.00	0.00	0.00	0	1191	0	0	0	0	8
4A1C_3	5S_rRNA links to Rfam database...	0.00	0.00	0.00	0	2763	0	0	0	0	37
4A1C_2	5_8S_rRNA links to Rfam database...	0.10	0.05	0.20	1	4511	23	0	4	19	19
4AOB_A	SAM links to Rfam database...	0.00	0.00	0.00	0	1437	0	0	0	0	29
4ENB_A	crcB links to Rfam database...	0.00	0.00	0.00	0	472	0	0	0	0	15
4ENC_A	crcB links to Rfam database...	0.00	0.00	0.00	0	496	0	0	0	0	15
4FRG_B	AdoCbl-variant links to Rfam database...	0.00	0.00	0.00	0	1202	0	0	0	0	24
4FRN_A	AdoCbl-variant links to Rfam database...	0.00	0.00	0.00	0	1848	0	0	0	0	28
4JF2_A	preQ1-II links to Rfam database...	0.76	0.63	0.94	15	1066	1	1	0	0	9

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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 PPfold(seed) - scored lower in this pairwise comparison

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

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