CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

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Overview

Metric	Pknots		PPfold(seed)
MCC	0.488	>	0.148
Average MCC ± 95% Confidence Intervals	0.535 ± 0.111	>	0.063 ± 0.066
Sensitivity	0.434	>	0.032
Positive Predictive Value	0.556	<	0.689
Total TP	419	>	31
Total TN	137375	<	138084
Total FP	384	>	75
Total FP CONTRA	25	>	0
Total FP INCONS	310	>	14
Total FP COMP	49	<	61
Total FN	546	<	934
P-value	5.10776592382e-08

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Performance plots

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

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Performance of Pknots - scored higher in this pairwise comparison

1. Total counts & total scores for Pknots

Total Base Pair Counts
Total TP	419
Total TN	137375
Total FP	384
Total FP CONTRA	25
Total FP INCONS	310
Total FP COMP	49
Total FN	546

Total Scores
MCC	0.488
Average MCC ± 95% Confidence Intervals	0.535 ± 0.111
Sensitivity	0.434
Positive Predictive Value	0.556
Nr of predictions	27

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2. Individual counts for Pknots [ 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...	0.79	0.75	0.83	15	1522	3	1	2	0	5
3AMU_B	tRNA links to Rfam database...	0.86	0.74	1.00	20	2983	2	0	0	2	7
3J16_L	tRNA links to Rfam database...	0.34	0.30	0.41	9	2753	13	0	13	0	21
3J20_1	tRNA links to Rfam database...	0.96	0.91	1.00	21	2905	0	0	0	0	2
3J20_0	tRNA links to Rfam database...	0.84	0.70	1.00	21	2829	1	0	0	1	9
3J2L_3	5S_rRNA links to Rfam database...	0.62	0.51	0.75	27	7839	12	0	9	3	26
3J3D_C	tRNA links to Rfam database...	0.46	0.43	0.50	12	2751	12	1	11	0	16
3J3E_8	5_8S_rRNA links to Rfam database...	0.07	0.06	0.08	2	7479	33	2	20	11	31
3J3E_7	5S_rRNA links to Rfam database...	0.43	0.35	0.54	19	7105	16	1	15	0	35
3J3F_7	5S_rRNA links to Rfam database...	0.27	0.24	0.32	12	7222	27	1	25	1	38
3J3F_8	5_8S_rRNA links to Rfam database...	0.36	0.36	0.37	13	12211	34	2	20	12	23
3RKF_A	Purine links to Rfam database...	0.77	0.62	0.95	21	2189	1	0	1	0	13
3SD1_A	THF links to Rfam database...	0.65	0.52	0.81	22	3889	5	0	5	0	20
3UZL_B	tRNA links to Rfam database...	0.75	0.59	0.96	22	3547	1	0	1	0	15
3W1K_J	tRNA-Sec links to Rfam database...	0.87	0.79	0.97	30	4155	1	1	0	0	8
3W3S_B	tRNA-Sec links to Rfam database...	0.71	0.63	0.81	25	4722	7	0	6	1	15
3ZEX_C	5_8S_rRNA links to Rfam database...	0.07	0.08	0.07	4	14141	54	4	47	3	48
3ZEX_D	5S_rRNA links to Rfam database...	0.27	0.24	0.30	12	6981	28	0	28	0	37
3ZND_W	tRNA links to Rfam database...	0.20	0.22	0.19	5	2977	23	1	20	2	18
4A1C_3	5S_rRNA links to Rfam database...	0.25	0.22	0.29	12	7099	29	1	28	0	42
4A1C_2	5_8S_rRNA links to Rfam database...	0.24	0.24	0.25	8	11749	36	3	21	12	25
4AOB_A	SAM links to Rfam database...	0.17	0.14	0.21	6	4343	23	1	21	1	36
4ENB_A	crcB links to Rfam database...	0.83	0.79	0.88	15	1258	2	1	1	0	4
4ENC_A	crcB links to Rfam database...	0.86	0.79	0.94	15	1310	1	1	0	0	4
4FRG_B	AdoCbl-variant links to Rfam database...	0.48	0.38	0.63	12	3467	7	0	7	0	20
4FRN_A	AdoCbl-variant links to Rfam database...	0.51	0.42	0.63	15	5127	9	1	8	0	21
4JF2_A	preQ1-II links to Rfam database...	0.81	0.77	0.86	24	2822	4	3	1	0	7

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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	31
Total TN	138084
Total FP	75
Total FP CONTRA	0
Total FP INCONS	14
Total FP COMP	61
Total FN	934

Total Scores
MCC	0.148
Average MCC ± 95% Confidence Intervals	0.063 ± 0.066
Sensitivity	0.032
Positive Predictive Value	0.689
Nr of predictions	27

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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...	0.47	0.30	0.75	6	1532	2	0	2	0	14
3AMU_B	tRNA links to Rfam database...	0.00	0.00	0.00	0	3003	0	0	0	0	27
3J16_L	tRNA links to Rfam database...	0.00	0.00	0.00	0	2775	0	0	0	0	30
3J20_1	tRNA links to Rfam database...	0.00	0.00	0.00	0	2926	0	0	0	0	23
3J20_0	tRNA links to Rfam database...	0.00	0.00	0.00	0	2850	0	0	0	0	30
3J2L_3	5S_rRNA links to Rfam database...	0.00	0.00	0.00	0	7875	0	0	0	0	53
3J3D_C	tRNA links to Rfam database...	0.00	0.00	0.00	0	2775	0	0	0	0	28
3J3E_8	5_8S_rRNA links to Rfam database...	0.00	0.00	0.00	0	7503	6	0	0	6	33
3J3E_7	5S_rRNA links to Rfam database...	0.00	0.00	0.00	0	7140	0	0	0	0	54
3J3F_7	5S_rRNA links to Rfam database...	0.00	0.00	0.00	0	7260	0	0	0	0	50
3J3F_8	5_8S_rRNA links to Rfam database...	0.23	0.11	0.50	4	12238	22	0	4	18	32
3RKF_A	Purine links to Rfam database...	0.00	0.00	0.00	0	2211	0	0	0	0	34
3SD1_A	THF links to Rfam database...	0.00	0.00	0.00	0	3916	0	0	0	0	42
3UZL_B	tRNA links to Rfam database...	0.00	0.00	0.00	0	3570	0	0	0	0	37
3W1K_J	tRNA-Sec links to Rfam database...	0.00	0.00	0.00	0	4186	0	0	0	0	38
3W3S_B	tRNA-Sec links to Rfam database...	0.00	0.00	0.00	0	4753	0	0	0	0	40
3ZEX_C	5_8S_rRNA links to Rfam database...	0.20	0.08	0.50	4	14188	22	0	4	18	48
3ZEX_D	5S_rRNA links to Rfam database...	0.00	0.00	0.00	0	7021	0	0	0	0	49
3ZND_W	tRNA links to Rfam database...	0.00	0.00	0.00	0	3003	0	0	0	0	23
4A1C_3	5S_rRNA links to Rfam database...	0.00	0.00	0.00	0	7140	0	0	0	0	54
4A1C_2	5_8S_rRNA links to Rfam database...	0.08	0.03	0.20	1	11776	23	0	4	19	32
4AOB_A	SAM links to Rfam database...	0.00	0.00	0.00	0	4371	0	0	0	0	42
4ENB_A	crcB links to Rfam database...	0.00	0.00	0.00	0	1275	0	0	0	0	19
4ENC_A	crcB links to Rfam database...	0.00	0.00	0.00	0	1326	0	0	0	0	19
4FRG_B	AdoCbl-variant links to Rfam database...	0.00	0.00	0.00	0	3486	0	0	0	0	32
4FRN_A	AdoCbl-variant links to Rfam database...	0.00	0.00	0.00	0	5151	0	0	0	0	36
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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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 Pknots - scored higher in this pairwise comparison

1. Total counts & total scores for Pknots

2. Individual counts for Pknots [ 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 ]