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	CentroidAlifold(seed)		Vsfold4
MCC	0.720	>	0.542
Average MCC ± 95% Confidence Intervals	0.686 ± 0.087	>	0.574 ± 0.130
Sensitivity	0.579	>	0.545
Positive Predictive Value	0.898	>	0.546
Total TP	423	>	398
Total TN	91207	>	90949
Total FP	80	<	401
Total FP CONTRA	40	<	112
Total FP INCONS	8	<	219
Total FP COMP	32	<	70
Total FN	307	<	332
P-value	5.06544643719e-08

^top

Performance plots

Comparison of performance of CentroidAlifold(seed) and Vsfold4. 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 CentroidAlifold(seed) and Vsfold4).
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 CentroidAlifold(seed) and Vsfold4).
Comparison of average Matthews Correlation Coefficients (MCCs) for CentroidAlifold(seed) and Vsfold4. 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 CentroidAlifold(seed) and Vsfold4).

^top

Performance of CentroidAlifold(seed) - scored higher in this pairwise comparison

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

Total Base Pair Counts
Total TP	423
Total TN	91207
Total FP	80
Total FP CONTRA	40
Total FP INCONS	8
Total FP COMP	32
Total FN	307

Total Scores
MCC	0.720
Average MCC ± 95% Confidence Intervals	0.686 ± 0.087
Sensitivity	0.579
Positive Predictive Value	0.898
Nr of predictions	26

^top

2. Individual counts for CentroidAlifold(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...	0.00	0.00	0.00	0	528	0	0	0	0	18
2ZZN_D	tRNA links to Rfam database...	0.52	0.27	1.00	6	978	0	0	0	0	16
3A2K_C	tRNA links to Rfam database...	0.52	0.27	1.00	6	1102	0	0	0	0	16
3A3A_A	tRNA-Sec links to Rfam database...	0.95	0.90	1.00	27	1473	0	0	0	0	3
3GX2_A	SAM links to Rfam database...	0.92	0.86	1.00	24	1425	1	0	0	1	4
3IVN_B	Purine links to Rfam database...	0.86	0.83	0.90	19	882	2	2	0	0	4
3IYQ_A	tmRNA links to Rfam database...	0.56	0.55	0.57	28	22391	30	19	2	9	23
3IZ4_A	tmRNA links to Rfam database...	0.58	0.43	0.77	41	25483	17	12	0	5	54
3J20_0	tRNA links to Rfam database...	0.53	0.29	1.00	6	1213	0	0	0	0	15
3J3D_C	tRNA links to Rfam database...	0.56	0.32	1.00	6	962	0	0	0	0	13
3J3E_8	5_8S_rRNA links to Rfam database...	0.39	0.20	0.75	3	2738	1	1	0	0	12
3J3F_8	5_8S_rRNA links to Rfam database...	0.62	0.47	0.82	9	4750	4	2	0	2	10
3JYV_7	tRNA links to Rfam database...	0.50	0.25	1.00	5	1106	1	0	0	1	15
3LA5_A	Purine links to Rfam database...	0.87	0.80	0.95	20	933	1	1	0	0	5
3NPB_A	SAM links to Rfam database...	0.79	0.65	0.96	24	2253	5	0	1	4	13
3O58_3	5_8S_rRNA links to Rfam database...	0.68	0.50	0.92	11	4752	2	1	0	1	11
3PDR_A	ykoK links to Rfam database...	0.93	0.88	0.98	44	4795	3	0	1	2	6
3RKF_A	Purine links to Rfam database...	0.91	0.83	1.00	20	846	0	0	0	0	4
3SD1_A	THF links to Rfam database...	0.85	0.76	0.96	22	1510	1	0	1	0	7
3W3S_B	tRNA-Sec links to Rfam database...	0.80	0.70	0.92	23	1964	4	0	2	2	10
4A1C_2	5_8S_rRNA links to Rfam database...	0.60	0.40	0.89	8	4507	3	1	0	2	12
4AOB_A	SAM links to Rfam database...	0.89	0.79	1.00	23	1414	2	0	0	2	6
4ENB_A	crcB links to Rfam database...	0.72	0.53	1.00	8	464	0	0	0	0	7
4ENC_A	crcB links to Rfam database...	0.73	0.53	1.00	8	488	0	0	0	0	7
4FRG_B	AdoCbl-variant links to Rfam database...	0.81	0.71	0.94	17	1184	2	0	1	1	7
4JF2_A	preQ1-II links to Rfam database...	0.76	0.63	0.94	15	1066	1	1	0	0	9

^top

Performance of Vsfold4 - scored lower in this pairwise comparison

1. Total counts & total scores for Vsfold4

Total Base Pair Counts
Total TP	398
Total TN	90949
Total FP	401
Total FP CONTRA	112
Total FP INCONS	219
Total FP COMP	70
Total FN	332

Total Scores
MCC	0.542
Average MCC ± 95% Confidence Intervals	0.574 ± 0.130
Sensitivity	0.545
Positive Predictive Value	0.546
Nr of predictions	26

^top

2. Individual counts for Vsfold4 [ 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...	-0.03	0.00	0.00	0	515	13	0	13	0	18
2ZZN_D	tRNA links to Rfam database...	0.95	0.95	0.95	21	962	1	1	0	0	1
3A2K_C	tRNA links to Rfam database...	0.95	0.91	1.00	20	1088	0	0	0	0	2
3A3A_A	tRNA-Sec links to Rfam database...	0.95	0.90	1.00	27	1473	0	0	0	0	3
3GX2_A	SAM links to Rfam database...	0.60	0.57	0.64	16	1424	10	0	9	1	12
3IVN_B	Purine links to Rfam database...	0.91	0.83	1.00	19	884	0	0	0	0	4
3IYQ_A	tmRNA links to Rfam database...	0.27	0.35	0.21	18	22353	80	40	29	11	33
3IZ4_A	tmRNA links to Rfam database...	0.39	0.39	0.39	37	25441	63	15	43	5	58
3J20_0	tRNA links to Rfam database...	0.95	0.95	0.95	20	1198	2	1	0	1	1
3J3D_C	tRNA links to Rfam database...	0.48	0.53	0.45	10	946	12	4	8	0	9
3J3E_8	5_8S_rRNA links to Rfam database...	0.10	0.13	0.09	2	2720	32	9	11	12	13
3J3F_8	5_8S_rRNA links to Rfam database...	0.35	0.42	0.30	8	4734	30	11	8	11	11
3JYV_7	tRNA links to Rfam database...	-0.02	0.00	0.00	0	1092	19	4	15	0	20
3LA5_A	Purine links to Rfam database...	0.91	0.84	1.00	21	933	0	0	0	0	4
3NPB_A	SAM links to Rfam database...	0.66	0.59	0.73	22	2248	10	0	8	2	15
3O58_3	5_8S_rRNA links to Rfam database...	0.12	0.14	0.11	3	4737	35	8	16	11	19
3PDR_A	ykoK links to Rfam database...	0.69	0.64	0.74	32	4797	13	3	8	2	18
3RKF_A	Purine links to Rfam database...	0.91	0.83	1.00	20	846	0	0	0	0	4
3SD1_A	THF links to Rfam database...	0.23	0.24	0.24	7	1504	22	5	17	0	22
3W3S_B	tRNA-Sec links to Rfam database...	0.74	0.70	0.79	23	1960	7	1	5	1	10
4A1C_2	5_8S_rRNA links to Rfam database...	0.36	0.40	0.33	8	4492	28	4	12	12	12
4AOB_A	SAM links to Rfam database...	0.50	0.48	0.54	14	1411	13	3	9	1	15
4ENB_A	crcB links to Rfam database...	0.85	0.73	1.00	11	461	0	0	0	0	4
4ENC_A	crcB links to Rfam database...	0.77	0.60	1.00	9	487	0	0	0	0	6
4FRG_B	AdoCbl-variant links to Rfam database...	0.60	0.58	0.64	14	1180	8	3	5	0	10
4JF2_A	preQ1-II links to Rfam database...	0.74	0.67	0.84	16	1063	3	0	3	0	8

^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 CentroidAlifold(seed) - scored higher in this pairwise comparison

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

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

Performance of Vsfold4 - scored lower in this pairwise comparison

1. Total counts & total scores for Vsfold4

2. Individual counts for Vsfold4 [ download as .csv ]