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)		CentroidFold
MCC	0.715	>	0.522
Average MCC ± 95% Confidence Intervals	0.699 ± 0.059	>	0.504 ± 0.092
Sensitivity	0.602	>	0.438
Positive Predictive Value	0.850	>	0.625
Total TP	935	>	679
Total TN	1251685	<	1251698
Total FP	203	<	441
Total FP CONTRA	18	<	35
Total FP INCONS	147	<	373
Total FP COMP	38	>	33
Total FN	617	<	873
P-value	5.19332990918e-08

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Performance plots

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

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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	935
Total TN	1251685
Total FP	203
Total FP CONTRA	18
Total FP INCONS	147
Total FP COMP	38
Total FN	617

Total Scores
MCC	0.715
Average MCC ± 95% Confidence Intervals	0.699 ± 0.059
Sensitivity	0.602
Positive Predictive Value	0.850
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
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_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
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 CentroidFold - scored lower in this pairwise comparison

1. Total counts & total scores for CentroidFold

Total Base Pair Counts
Total TP	679
Total TN	1251698
Total FP	441
Total FP CONTRA	35
Total FP INCONS	373
Total FP COMP	33
Total FN	873

Total Scores
MCC	0.522
Average MCC ± 95% Confidence Intervals	0.504 ± 0.092
Sensitivity	0.438
Positive Predictive Value	0.625
Nr of predictions	26

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2. Individual counts for CentroidFold [ 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	0.35	0.70	7	1530	3	1	2	0	13
3J16_L	tRNA links to Rfam database...	0.50	0.40	0.63	12	2756	7	0	7	0	18
3J20_0	tRNA links to Rfam database...	0.44	0.40	0.50	12	2826	13	0	12	1	18
3J20_1	tRNA links to Rfam database...	0.91	0.87	0.95	20	2905	2	0	1	1	3
3J20_2	SSU_rRNA_archaea links to Rfam database...	0.56	0.48	0.67	303	1116310	158	8	144	6	330
3J2L_3	5S_rRNA links to Rfam database...	0.53	0.49	0.58	26	7830	21	0	19	2	27
3J3D_C	tRNA links to Rfam database...	0.49	0.43	0.57	12	2754	9	0	9	0	16
3J3E_8	5_8S_rRNA links to Rfam database...	0.00	0.00	0.00	0	7485	21	2	16	3	33
3J3E_7	5S_rRNA links to Rfam database...	0.46	0.37	0.59	20	7106	14	1	13	0	34
3J3F_7	5S_rRNA links to Rfam database...	0.20	0.18	0.23	9	7221	30	1	29	0	41
3J3F_8	5_8S_rRNA links to Rfam database...	0.34	0.33	0.34	12	12211	34	4	19	11	24
3J3V_B	5S_rRNA links to Rfam database...	0.47	0.37	0.60	21	6986	14	1	13	0	36
3UZL_B	tRNA links to Rfam database...	0.72	0.54	0.95	20	3549	1	0	1	0	17
3W1K_J	tRNA-Sec links to Rfam database...	0.56	0.50	0.63	19	4156	11	2	9	0	19
3W3S_B	tRNA-Sec links to Rfam database...	0.87	0.78	0.97	31	4721	2	0	1	1	9
3ZEX_C	5_8S_rRNA links to Rfam database...	0.47	0.27	0.82	14	14179	3	1	2	0	38
3ZEX_D	5S_rRNA links to Rfam database...	0.73	0.59	0.91	29	6989	3	0	3	0	20
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...	0.67	0.56	0.81	30	7103	7	1	6	0	24
4A1C_2	5_8S_rRNA links to Rfam database...	0.16	0.15	0.17	5	11752	29	5	19	5	28
4AOB_A	SAM links to Rfam database...	0.45	0.33	0.61	14	4348	10	1	8	1	28
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...	0.73	0.58	0.92	11	1314	1	1	0	0	8
4FRG_B	AdoCbl-variant links to Rfam database...	0.24	0.22	0.28	7	3461	18	3	15	0	25
4FRN_A	AdoCbl-variant links to Rfam database...	0.40	0.28	0.59	10	5134	7	2	5	0	26
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 CentroidFold - scored lower in this pairwise comparison

1. Total counts & total scores for CentroidFold

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