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	Sfold		RSpredict(seed)
MCC	0.541	>	0.337
Average MCC ± 95% Confidence Intervals	0.571 ± 0.065	>	0.148 ± 0.068
Sensitivity	0.461	>	0.189
Positive Predictive Value	0.635	>	0.603
Total TP	1161	>	476
Total TN	1486908	<	1487946
Total FP	765	>	322
Total FP CONTRA	75	>	23
Total FP INCONS	591	>	290
Total FP COMP	99	>	9
Total FN	1358	<	2043
P-value	3.56938820447e-08

^top

Performance plots

Comparison of performance of Sfold 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 Sfold 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 Sfold and RSpredict(seed)).
Comparison of average Matthews Correlation Coefficients (MCCs) for Sfold 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 Sfold and RSpredict(seed)).

^top

Performance of Sfold - scored higher in this pairwise comparison

1. Total counts & total scores for Sfold

Total Base Pair Counts
Total TP	1161
Total TN	1486908
Total FP	765
Total FP CONTRA	75
Total FP INCONS	591
Total FP COMP	99
Total FN	1358

Total Scores
MCC	0.541
Average MCC ± 95% Confidence Intervals	0.571 ± 0.065
Sensitivity	0.461
Positive Predictive Value	0.635
Nr of predictions	51

^top

2. Individual counts for Sfold [ 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	0.91	1.00	10	396	0	0	0	0	1
2KX8_A	7SK links to Rfam database...	0.94	0.89	1.00	16	845	0	0	0	0	2
2LC8_A	GP_knot1 links to Rfam database...	0.45	0.35	0.58	7	1528	5	0	5	0	13
2WRQ_Y	tRNA links to Rfam database...	0.53	0.53	0.53	9	2833	13	5	3	5	8
2WWQ_V	tRNA links to Rfam database...	0.80	0.68	0.95	19	2906	2	0	1	1	9
2XQD_Y	tRNA links to Rfam database...	0.77	0.67	0.90	18	2830	2	0	2	0	9
2ZZM_B	tRNA links to Rfam database...	0.12	0.09	0.17	3	3468	15	0	15	0	29
2ZZN_D	tRNA links to Rfam database...	0.82	0.78	0.88	21	2461	3	0	3	0	6
3A2K_C	tRNA links to Rfam database...	0.42	0.39	0.46	11	2902	13	2	11	0	17
3A3A_A	tRNA-Sec links to Rfam database...	0.87	0.76	1.00	28	3627	0	0	0	0	9
3AKZ_H	tRNA links to Rfam database...	0.44	0.39	0.50	11	2679	11	2	9	0	17
3AMU_B	tRNA links to Rfam database...	0.70	0.59	0.84	16	2984	5	0	3	2	11
3GX2_A	SAM links to Rfam database...	0.72	0.55	0.96	22	4348	2	0	1	1	18
3IVN_B	Purine links to Rfam database...	0.78	0.61	1.00	19	2327	0	0	0	0	12
3IYQ_A	tmRNA links to Rfam database...	0.33	0.34	0.32	32	60627	71	19	48	4	62
3IZ4_A	tmRNA links to Rfam database...	0.52	0.42	0.65	56	70790	31	3	27	1	76
3IZF_C	5S_rRNA links to Rfam database...	0.71	0.61	0.83	33	6863	7	0	7	0	21
3J16_L	tRNA links to Rfam database...	0.29	0.23	0.37	7	2756	12	0	12	0	23
3J20_1	tRNA links to Rfam database...	0.73	0.70	0.76	16	2905	6	0	5	1	7
3J20_0	tRNA links to Rfam database...	0.43	0.40	0.48	12	2825	14	0	13	1	18
3J20_2	SSU_rRNA_archaea links to Rfam database...	0.47	0.41	0.55	261	1116287	220	14	203	3	372
3J2L_3	5S_rRNA links to Rfam database...	0.62	0.53	0.74	28	7837	12	0	10	2	25
3J3D_C	tRNA links to Rfam database...	0.36	0.25	0.54	7	2762	6	0	6	0	21
3J3E_7	5S_rRNA links to Rfam database...	0.60	0.50	0.73	27	7103	10	1	9	0	27
3J3E_8	5_8S_rRNA links to Rfam database...	0.06	0.06	0.08	2	7477	32	2	22	8	31
3J3F_8	5_8S_rRNA links to Rfam database...	0.35	0.33	0.38	12	12214	34	3	17	14	24
3J3F_7	5S_rRNA links to Rfam database...	0.69	0.60	0.79	30	7222	8	1	7	0	20
3JYV_7	tRNA links to Rfam database...	-0.01	0.00	0.00	0	2834	16	0	16	0	32
3JYX_4	5_8S_rRNA links to Rfam database...	0.35	0.30	0.42	10	12222	23	3	11	9	23
3JYX_3	5S_rRNA links to Rfam database...	0.62	0.63	0.61	17	6300	19	1	10	8	10
3LA5_A	Purine links to Rfam database...	0.78	0.62	1.00	21	2464	0	0	0	0	13
3NPB_A	SAM links to Rfam database...	0.77	0.65	0.91	30	6988	6	1	2	3	16
3O58_2	5S_rRNA links to Rfam database...	0.74	0.74	0.74	28	7222	11	3	7	1	10
3O58_3	5_8S_rRNA links to Rfam database...	0.43	0.34	0.55	12	12381	17	0	10	7	23
3PDR_A	ykoK links to Rfam database...	0.69	0.56	0.85	40	12833	9	0	7	2	32
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...	0.65	0.50	0.84	21	3891	4	1	3	0	21
3UZL_B	tRNA links to Rfam database...	0.51	0.32	0.80	12	3555	3	2	1	0	25
3W1K_J	tRNA-Sec links to Rfam database...	0.87	0.79	0.97	30	4155	1	1	0	0	8
3W3S_B	tRNA-Sec links to Rfam database...	0.57	0.53	0.64	21	4720	13	1	11	1	19
3ZEX_D	5S_rRNA links to Rfam database...	0.74	0.63	0.86	31	6985	5	0	5	0	18
3ZEX_C	5_8S_rRNA links to Rfam database...	0.32	0.21	0.48	11	14173	26	1	11	14	41
3ZND_W	tRNA links to Rfam database...	0.20	0.22	0.19	5	2977	22	1	20	1	18
4A1C_2	5_8S_rRNA links to Rfam database...	0.16	0.15	0.17	5	11751	34	2	23	9	28
4A1C_3	5S_rRNA links to Rfam database...	0.69	0.57	0.84	31	7103	6	1	5	0	23
4AOB_A	SAM links to Rfam database...	0.50	0.40	0.63	17	4344	11	2	8	1	25
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...	0.51	0.26	1.00	5	1321	0	0	0	0	14
4FRG_B	AdoCbl-variant links to Rfam database...	0.62	0.47	0.83	15	3468	3	1	2	0	17
4FRN_A	AdoCbl-variant links to Rfam database...	0.63	0.44	0.89	16	5133	2	2	0	0	20
4JF2_A	preQ1-II links to Rfam database...	0.78	0.61	1.00	19	2831	0	0	0	0	12

^top

Performance of RSpredict(seed) - scored lower in this pairwise comparison

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

Total Base Pair Counts
Total TP	476
Total TN	1487946
Total FP	322
Total FP CONTRA	23
Total FP INCONS	290
Total FP COMP	9
Total FN	2043

Total Scores
MCC	0.337
Average MCC ± 95% Confidence Intervals	0.148 ± 0.068
Sensitivity	0.189
Positive Predictive Value	0.603
Nr of predictions	51

^top

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
2KDQ_B	mir-TAR links to Rfam database...	0.85	0.73	1.00	8	398	0	0	0	0	3
2KX8_A	7SK links to Rfam database...	0.00	0.00	0.00	0	860	1	0	1	0	18
2LC8_A	GP_knot1 links to Rfam database...	-0.01	0.00	0.00	0	1527	13	0	13	0	20
2WRQ_Y	tRNA links to Rfam database...	0.00	0.00	0.00	0	2848	3	1	1	1	17
2WWQ_V	tRNA links to Rfam database...	0.00	0.00	0.00	0	2920	6	1	5	0	28
2XQD_Y	tRNA links to Rfam database...	0.00	0.00	0.00	0	2845	5	0	5	0	27
2ZZM_B	tRNA links to Rfam database...	0.00	0.00	0.00	0	3482	4	0	4	0	32
2ZZN_D	tRNA links to Rfam database...	0.43	0.19	1.00	5	2480	0	0	0	0	22
3A2K_C	tRNA links to Rfam database...	0.00	0.00	0.00	0	2924	2	0	2	0	28
3A3A_A	tRNA-Sec links to Rfam database...	0.48	0.30	0.79	11	3641	3	0	3	0	26
3AKZ_H	tRNA links to Rfam database...	0.00	0.00	0.00	0	2699	2	0	2	0	28
3AMU_B	tRNA links to Rfam database...	0.00	0.00	0.00	0	3001	2	0	2	0	27
3GX2_A	SAM links to Rfam database...	0.36	0.15	0.86	6	4364	1	0	1	0	34
3IVN_B	Purine links to Rfam database...	0.69	0.52	0.94	16	2329	1	0	1	0	15
3IYQ_A	tmRNA links to Rfam database...	0.14	0.07	0.28	7	60701	19	5	13	1	87
3IZ4_A	tmRNA links to Rfam database...	0.21	0.08	0.59	10	70859	7	0	7	0	122
3IZF_C	5S_rRNA links to Rfam database...	0.00	0.00	0.00	0	6898	5	0	5	0	54
3J16_L	tRNA links to Rfam database...	0.00	0.00	0.00	0	2774	1	0	1	0	30
3J20_1	tRNA links to Rfam database...	0.09	0.04	0.20	1	2921	4	0	4	0	22
3J20_0	tRNA links to Rfam database...	0.00	0.00	0.00	0	2846	4	0	4	0	30
3J20_2	SSU_rRNA_archaea links to Rfam database...	0.62	0.53	0.73	335	1116304	129	9	117	3	298
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_7	5S_rRNA links to Rfam database...	0.00	0.00	0.00	0	7132	8	0	8	0	54
3J3E_8	5_8S_rRNA links to Rfam database...	0.00	0.00	0.00	0	7503	0	0	0	0	33
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
3JYV_7	tRNA links to Rfam database...	0.00	0.00	0.00	0	2846	4	0	4	0	32
3JYX_4	5_8S_rRNA links to Rfam database...	0.00	0.00	0.00	0	12241	5	0	5	0	33
3JYX_3	5S_rRNA links to Rfam database...	0.00	0.00	0.00	0	6323	5	1	4	0	27
3LA5_A	Purine links to Rfam database...	0.70	0.50	1.00	17	2468	0	0	0	0	17
3NPB_A	SAM links to Rfam database...	0.00	0.00	0.00	0	7017	4	0	4	0	46
3O58_2	5S_rRNA links to Rfam database...	0.00	0.00	0.00	0	7257	3	0	3	0	38
3O58_3	5_8S_rRNA links to Rfam database...	0.23	0.09	0.60	3	12398	2	0	2	0	32
3PDR_A	ykoK links to Rfam database...	0.00	0.00	0.00	0	12872	8	0	8	0	72
3RKF_A	Purine links to Rfam database...	0.71	0.53	0.95	18	2192	1	0	1	0	16
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	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_D	5S_rRNA links to Rfam database...	0.00	0.00	0.00	0	7019	2	0	2	0	49
3ZEX_C	5_8S_rRNA links to Rfam database...	0.10	0.04	0.25	2	14188	6	1	5	0	50
3ZND_W	tRNA links to Rfam database...	0.00	0.00	0.00	0	3000	4	0	3	1	23
4A1C_2	5_8S_rRNA links to Rfam database...	0.00	0.00	0.00	0	11777	5	1	3	1	33
4A1C_3	5S_rRNA links to Rfam database...	0.00	0.00	0.00	0	7136	4	1	3	0	54
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

^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 Sfold - scored higher in this pairwise comparison

1. Total counts & total scores for Sfold

2. Individual counts for Sfold [ 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 ]