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	RNAalifold(20)		Vsfold5
MCC	0.802	>	0.494
Average MCC ± 95% Confidence Intervals	0.793 ± 0.071	>	0.546 ± 0.126
Sensitivity	0.714	>	0.496
Positive Predictive Value	0.904	>	0.503
Total TP	619	>	430
Total TN	86803	>	86633
Total FP	158	<	521
Total FP CONTRA	22	<	116
Total FP INCONS	44	<	309
Total FP COMP	92	<	96
Total FN	248	<	437
P-value	3.56938820447e-08

^top

Performance plots

Comparison of performance of RNAalifold(20) and Vsfold5. 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 RNAalifold(20) and Vsfold5).
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 RNAalifold(20) and Vsfold5).
Comparison of average Matthews Correlation Coefficients (MCCs) for RNAalifold(20) and Vsfold5. 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 RNAalifold(20) and Vsfold5).

^top

Performance of RNAalifold(20) - scored higher in this pairwise comparison

1. Total counts & total scores for RNAalifold(20)

Total Base Pair Counts
Total TP	619
Total TN	86803
Total FP	158
Total FP CONTRA	22
Total FP INCONS	44
Total FP COMP	92
Total FN	248

Total Scores
MCC	0.802
Average MCC ± 95% Confidence Intervals	0.793 ± 0.071
Sensitivity	0.714
Positive Predictive Value	0.904
Nr of predictions	33

^top

2. Individual counts for RNAalifold(20) [ download as .csv ]

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2KDQ_B	mir-TAR links to Rfam database...	0.62	0.40	1.00	4	170	0	0	0	0	6
2L94_A	HIV_FE links to Rfam database...	0.51	0.50	0.56	9	341	8	0	7	1	9
2WRQ_Y	tRNA links to Rfam database...	1.00	1.00	1.00	9	1143	12	0	0	12	0
2XKV_B	Bacteria_small_SRP links to Rfam database...	0.60	0.36	1.00	4	1831	3	0	0	3	7
2XQD_Y	tRNA links to Rfam database...	0.98	0.95	1.00	20	1109	1	0	0	1	1
2XXA_G	Bacteria_small_SRP links to Rfam database...	0.44	0.20	1.00	7	2038	0	0	0	0	28
3A2K_C	tRNA links to Rfam database...	0.98	0.95	1.00	21	1087	0	0	0	0	1
3AMU_B	tRNA links to Rfam database...	1.00	1.00	1.00	19	1138	2	0	0	2	0
3G4S_9	5S_rRNA links to Rfam database...	0.96	0.92	1.00	24	2712	7	0	0	7	2
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	0.78	0.95	18	884	1	1	0	0	5
3IZ4_A	tmRNA links to Rfam database...	0.65	0.48	0.87	46	25483	15	4	3	8	49
3IZF_C	5S_rRNA links to Rfam database...	0.90	0.89	0.91	31	2606	6	0	3	3	4
3J20_0	tRNA links to Rfam database...	0.95	0.95	0.95	20	1198	1	1	0	0	1
3J20_1	tRNA links to Rfam database...	1.00	1.00	1.00	20	1092	1	0	0	1	0
3J2L_3	5S_rRNA links to Rfam database...	0.86	0.74	1.00	25	2995	2	0	0	2	9
3JYV_7	tRNA links to Rfam database...	0.97	0.95	1.00	19	1092	2	0	0	2	1
3JYX_3	5S_rRNA links to Rfam database...	0.76	0.73	0.79	11	2364	20	0	3	17	4
3JYX_4	5_8S_rRNA links to Rfam database...	0.77	0.83	0.71	10	4742	15	3	1	11	2
3LA5_A	Purine links to Rfam database...	0.87	0.76	1.00	19	935	0	0	0	0	6
3NPB_A	SAM links to Rfam database...	0.75	0.57	1.00	21	2257	4	0	0	4	16
3O58_3	5_8S_rRNA links to Rfam database...	0.42	0.36	0.50	8	4748	9	3	5	1	14
3O58_2	5S_rRNA links to Rfam database...	0.97	0.94	1.00	29	2725	7	0	0	7	2
3PDR_A	ykoK links to Rfam database...	0.92	0.88	0.96	44	4794	3	1	1	1	6
3RKF_A	Purine links to Rfam database...	0.81	0.71	0.94	17	848	1	0	1	0	7
3SD1_A	THF links to Rfam database...	0.84	0.86	0.83	25	1503	5	4	1	0	4
3ZEX_D	5S_rRNA links to Rfam database...	0.91	0.89	0.94	31	2763	6	0	2	4	4
4A1C_3	5S_rRNA links to Rfam database...	0.90	0.84	0.97	31	2731	1	0	1	0	6
4A1C_2	5_8S_rRNA links to Rfam database...	0.22	0.25	0.19	5	4490	23	5	16	2	15
4AOB_A	SAM links to Rfam database...	0.85	0.72	1.00	21	1416	2	0	0	2	8
4ENB_A	crcB links to Rfam database...	0.51	0.27	1.00	4	468	0	0	0	0	11
4ENC_A	crcB links to Rfam database...	0.63	0.40	1.00	6	490	0	0	0	0	9
4FRG_B	AdoCbl-variant links to Rfam database...	0.84	0.71	1.00	17	1185	0	0	0	0	7

^top

Performance of Vsfold5 - scored lower in this pairwise comparison

1. Total counts & total scores for Vsfold5

Total Base Pair Counts
Total TP	430
Total TN	86633
Total FP	521
Total FP CONTRA	116
Total FP INCONS	309
Total FP COMP	96
Total FN	437

Total Scores
MCC	0.494
Average MCC ± 95% Confidence Intervals	0.546 ± 0.126
Sensitivity	0.496
Positive Predictive Value	0.503
Nr of predictions	33

^top

2. Individual counts for Vsfold5 [ download as .csv ]

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2KDQ_B	mir-TAR links to Rfam database...	0.95	0.90	1.00	9	165	0	0	0	0	1
2L94_A	HIV_FE links to Rfam database...	0.97	0.94	1.00	17	340	1	0	0	1	1
2WRQ_Y	tRNA links to Rfam database...	0.94	0.89	1.00	8	1144	13	0	0	13	1
2XKV_B	Bacteria_small_SRP links to Rfam database...	-0.01	0.00	0.00	0	1803	32	17	15	0	11
2XQD_Y	tRNA links to Rfam database...	0.95	0.90	1.00	19	1110	1	0	0	1	2
2XXA_G	Bacteria_small_SRP links to Rfam database...	-0.02	0.00	0.00	0	2014	31	2	29	0	35
3A2K_C	tRNA links to Rfam database...	0.95	0.91	1.00	20	1088	0	0	0	0	2
3AMU_B	tRNA links to Rfam database...	0.77	0.79	0.75	15	1137	8	0	5	3	4
3G4S_9	5S_rRNA links to Rfam database...	0.12	0.15	0.11	4	2699	33	9	24	0	22
3GX2_A	SAM links to Rfam database...	0.61	0.57	0.67	16	1425	9	0	8	1	12
3IVN_B	Purine links to Rfam database...	0.88	0.78	1.00	18	885	0	0	0	0	5
3IZ4_A	tmRNA links to Rfam database...	0.31	0.31	0.33	29	25448	65	14	45	6	66
3IZF_C	5S_rRNA links to Rfam database...	0.85	0.83	0.88	29	2607	5	0	4	1	6
3J20_0	tRNA links to Rfam database...	0.76	0.76	0.76	16	1198	6	3	2	1	5
3J20_1	tRNA links to Rfam database...	0.75	0.75	0.75	15	1092	7	0	5	2	5
3J2L_3	5S_rRNA links to Rfam database...	0.70	0.71	0.71	24	2986	13	3	7	3	10
3JYV_7	tRNA links to Rfam database...	-0.02	0.00	0.00	0	1092	19	4	15	0	20
3JYX_3	5S_rRNA links to Rfam database...	0.12	0.13	0.11	2	2360	20	6	10	4	13
3JYX_4	5_8S_rRNA links to Rfam database...	0.63	0.83	0.48	10	4735	32	9	2	21	2
3LA5_A	Purine links to Rfam database...	-0.02	0.00	0.00	0	938	16	0	16	0	25
3NPB_A	SAM links to Rfam database...	0.62	0.54	0.71	20	2250	10	1	7	2	17
3O58_3	5_8S_rRNA links to Rfam database...	0.51	0.59	0.45	13	4735	28	11	5	12	9
3O58_2	5S_rRNA links to Rfam database...	0.50	0.52	0.50	16	2722	19	3	13	3	15
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...	0.90	0.92	0.88	22	841	3	3	0	0	2
3SD1_A	THF links to Rfam database...	0.13	0.14	0.15	4	1507	22	5	17	0	25
3ZEX_D	5S_rRNA links to Rfam database...	0.09	0.09	0.12	3	2771	24	5	17	2	32
4A1C_3	5S_rRNA links to Rfam database...	0.29	0.30	0.31	11	2727	26	4	21	1	26
4A1C_2	5_8S_rRNA links to Rfam database...	0.33	0.40	0.28	8	4487	37	8	13	16	12
4AOB_A	SAM links to Rfam database...	0.21	0.21	0.25	6	1413	19	2	16	1	23
4ENB_A	crcB links to Rfam database...	1.00	1.00	1.00	15	457	0	0	0	0	0
4ENC_A	crcB links to Rfam database...	0.97	1.00	0.94	15	480	1	1	0	0	0
4FRG_B	AdoCbl-variant links to Rfam database...	0.60	0.58	0.64	14	1180	8	3	5	0	10

^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 RNAalifold(20) - scored higher in this pairwise comparison

1. Total counts & total scores for RNAalifold(20)

2. Individual counts for RNAalifold(20) [ download as .csv ]

Performance of Vsfold5 - scored lower in this pairwise comparison

1. Total counts & total scores for Vsfold5

2. Individual counts for Vsfold5 [ download as .csv ]