CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

Home

Methods

Datasets

Rankings

RNA 2D Atlas

Help

FAQ

Contact us

RSS feeds

Twitter

Overview

Metric	CentroidFold		PPfold(seed)
MCC	0.511	>	0.148
Average MCC ± 95% Confidence Intervals	0.523 ± 0.092	>	0.063 ± 0.066
Sensitivity	0.426	>	0.032
Positive Predictive Value	0.619	<	0.689
Total TP	411	>	31
Total TN	137465	<	138084
Total FP	282	>	75
Total FP CONTRA	27	>	0
Total FP INCONS	226	>	14
Total FP COMP	29	<	61
Total FN	554	<	934
P-value	5.23657817852e-08

^top

Performance plots

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

^top

Performance of CentroidFold - scored higher in this pairwise comparison

1. Total counts & total scores for CentroidFold

Total Base Pair Counts
Total TP	411
Total TN	137465
Total FP	282
Total FP CONTRA	27
Total FP INCONS	226
Total FP COMP	29
Total FN	554

Total Scores
MCC	0.511
Average MCC ± 95% Confidence Intervals	0.523 ± 0.092
Sensitivity	0.426
Positive Predictive Value	0.619
Nr of predictions	27

^top

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
3AMU_B	tRNA links to Rfam database...	0.70	0.59	0.84	16	2984	5	0	3	2	11
3J16_L	tRNA links to Rfam database...	0.50	0.40	0.63	12	2756	7	0	7	0	18
3J20_1	tRNA links to Rfam database...	0.91	0.87	0.95	20	2905	2	0	1	1	3
3J20_0	tRNA links to Rfam database...	0.44	0.40	0.50	12	2826	13	0	12	1	18
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
3RKF_A	Purine links to Rfam database...	0.76	0.59	1.00	20	2191	0	0	0	0	14
3SD1_A	THF links to Rfam database...	0.58	0.48	0.71	20	3888	8	1	7	0	22
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

^top

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

^top

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

^top

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 CentroidFold - scored higher in this pairwise comparison

1. Total counts & total scores for CentroidFold

2. Individual counts for CentroidFold [ 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 ]