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)		RSpredict(seed)
MCC	0.688	>	0.416
Average MCC ± 95% Confidence Intervals	0.693 ± 0.060	>	0.125 ± 0.080
Sensitivity	0.566	>	0.264
Positive Predictive Value	0.838	>	0.659
Total TP	1105	>	515
Total TN	1673646	<	1674183
Total FP	253	<	275
Total FP CONTRA	24	>	18
Total FP INCONS	190	<	249
Total FP COMP	39	>	8
Total FN	847	<	1437
P-value	5.23657817852e-08

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Performance plots

Comparison of performance of PETfold_pre2.0(seed) and RSpredict(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 RSpredict(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 RSpredict(seed)).
Comparison of average Matthews Correlation Coefficients (MCCs) for PETfold_pre2.0(seed) and RSpredict(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 RSpredict(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	1105
Total TN	1673646
Total FP	253
Total FP CONTRA	24
Total FP INCONS	190
Total FP COMP	39
Total FN	847

Total Scores
MCC	0.688
Average MCC ± 95% Confidence Intervals	0.693 ± 0.060
Sensitivity	0.566
Positive Predictive Value	0.838
Nr of predictions	26

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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
3J20_2	SSU_rRNA_archaea links to Rfam database...	0.71	0.61	0.81	388	1116287	97	10	80	7	245
3J2C_N	SSU_rRNA_bacteria links to Rfam database...	0.60	0.45	0.80	205	428945	53	6	45	2	252
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_8	5_8S_rRNA links to Rfam database...	0.43	0.30	0.63	10	7487	8	0	6	2	23
3J3E_7	5S_rRNA links to Rfam database...	0.78	0.67	0.92	36	7101	3	0	3	0	18
3J3F_8	5_8S_rRNA links to Rfam database...	0.63	0.53	0.76	19	12221	10	0	6	4	17
3J3F_7	5S_rRNA links to Rfam database...	0.85	0.74	0.97	37	7222	2	0	1	1	13
3UZL_B	tRNA links to Rfam database...	0.72	0.54	0.95	20	3549	2	1	0	1	17
3W1K_J	tRNA-Sec links to Rfam database...	0.80	0.68	0.93	26	4158	3	1	1	1	12
3W3S_B	tRNA-Sec links to Rfam database...	0.78	0.65	0.93	26	4725	4	0	2	2	14
3ZEX_C	5_8S_rRNA links to Rfam database...	0.53	0.37	0.76	19	14171	10	1	5	4	33
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_3	5S_rRNA links to Rfam database...	0.83	0.70	0.97	38	7101	1	0	1	0	16
4A1C_2	5_8S_rRNA links to Rfam database...	0.57	0.45	0.71	15	11760	12	0	6	6	18
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 RSpredict(seed) - scored lower in this pairwise comparison

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

Total Base Pair Counts
Total TP	515
Total TN	1674183
Total FP	275
Total FP CONTRA	18
Total FP INCONS	249
Total FP COMP	8
Total FN	1437

Total Scores
MCC	0.416
Average MCC ± 95% Confidence Intervals	0.125 ± 0.080
Sensitivity	0.264
Positive Predictive Value	0.659
Nr of predictions	26

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2. Individual counts for RSpredict(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...	-0.01	0.00	0.00	0	1527	13	0	13	0	20
3J16_L	tRNA links to Rfam database...	0.00	0.00	0.00	0	2774	1	0	1	0	30
3J20_0	tRNA links to Rfam database...	0.00	0.00	0.00	0	2846	4	0	4	0	30
3J20_1	tRNA links to Rfam database...	0.09	0.04	0.20	1	2921	4	0	4	0	22
3J20_2	SSU_rRNA_archaea links to Rfam database...	0.62	0.53	0.73	335	1116304	129	9	117	3	298
3J2C_N	SSU_rRNA_bacteria links to Rfam database...	0.48	0.31	0.76	140	429016	46	3	42	1	317
3J2L_3	5S_rRNA links to Rfam database...	0.00	0.00	0.00	0	7870	5	0	5	0	53
3J3D_C	tRNA links to Rfam database...	0.00	0.00	0.00	0	2771	4	1	3	0	28
3J3E_8	5_8S_rRNA links to Rfam database...	0.00	0.00	0.00	0	7503	0	0	0	0	33
3J3E_7	5S_rRNA links to Rfam database...	0.00	0.00	0.00	0	7132	8	0	8	0	54
3J3F_8	5_8S_rRNA links to Rfam database...	0.14	0.06	0.33	2	12240	5	1	3	1	34
3J3F_7	5S_rRNA links to Rfam database...	0.00	0.00	0.00	0	7256	4	0	4	0	50
3UZL_B	tRNA links to Rfam database...	0.00	0.00	0.00	0	3564	6	0	6	0	37
3W1K_J	tRNA-Sec links to Rfam database...	0.51	0.29	0.92	11	4174	1	0	1	0	27
3W3S_B	tRNA-Sec links to Rfam database...	0.41	0.30	0.57	12	4732	10	1	8	1	28
3ZEX_C	5_8S_rRNA links to Rfam database...	0.10	0.04	0.25	2	14188	6	1	5	0	50
3ZEX_D	5S_rRNA links to Rfam database...	0.00	0.00	0.00	0	7019	2	0	2	0	49
3ZND_W	tRNA links to Rfam database...	0.00	0.00	0.00	0	3000	4	0	3	1	23
4A1C_3	5S_rRNA links to Rfam database...	0.00	0.00	0.00	0	7136	4	1	3	0	54
4A1C_2	5_8S_rRNA links to Rfam database...	0.00	0.00	0.00	0	11777	5	1	3	1	33
4AOB_A	SAM links to Rfam database...	0.35	0.14	0.86	6	4364	1	0	1	0	36
4ENB_A	crcB links to Rfam database...	0.30	0.16	0.60	3	1270	2	0	2	0	16
4ENC_A	crcB links to Rfam database...	0.30	0.16	0.60	3	1321	2	0	2	0	16
4FRG_B	AdoCbl-variant links to Rfam database...	0.00	0.00	0.00	0	3484	2	0	2	0	32
4FRN_A	AdoCbl-variant links to Rfam database...	0.00	0.00	0.00	0	5148	3	0	3	0	36
4JF2_A	preQ1-II links to Rfam database...	0.00	0.00	0.00	0	2846	4	0	4	0	31

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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 RSpredict(seed) - scored lower in this pairwise comparison

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

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