CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

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Overview

Metric	Vsfold4		RSpredict(seed)
MCC	0.517	>	0.314
Average MCC ± 95% Confidence Intervals	0.580 ± 0.094	>	0.284 ± 0.100
Sensitivity	0.445	>	0.161
Positive Predictive Value	0.605	<	0.620
Total TP	673	>	243
Total TN	296202	<	296923
Total FP	500	>	156
Total FP CONTRA	54	>	12
Total FP INCONS	386	>	137
Total FP COMP	60	>	7
Total FN	840	<	1270
P-value	3.56938820447e-08

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Performance plots

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

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Performance of Vsfold4 - scored higher in this pairwise comparison

1. Total counts & total scores for Vsfold4

Total Base Pair Counts
Total TP	673
Total TN	296202
Total FP	500
Total FP CONTRA	54
Total FP INCONS	386
Total FP COMP	60
Total FN	840

Total Scores
MCC	0.517
Average MCC ± 95% Confidence Intervals	0.580 ± 0.094
Sensitivity	0.445
Positive Predictive Value	0.605
Nr of predictions	44

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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
2KDQ_B	mir-TAR links to Rfam database...	0.95	0.91	1.00	10	396	0	0	0	0	1
2KE6_A	K10_TLS links to Rfam database...	0.97	0.95	1.00	18	1110	1	0	0	1	1
2KUR_A	K10_TLS links to Rfam database...	0.95	0.90	1.00	19	1109	0	0	0	0	2
2KUU_A	K10_TLS links to Rfam database...	0.92	0.86	1.00	18	1110	1	0	0	1	3
2KUV_A	K10_TLS links to Rfam database...	0.93	0.86	1.00	19	1109	0	0	0	0	3
2KUW_A	K10_TLS links to Rfam database...	0.95	0.90	1.00	19	1109	0	0	0	0	2
2KX8_A	7SK links to Rfam database...	0.94	0.89	1.00	16	845	0	0	0	0	2
2L1F_A	Gammaretro_CES links to Rfam database...	0.66	0.54	0.81	13	2064	3	0	3	0	11
2L1F_B	Gammaretro_CES links to Rfam database...	0.68	0.56	0.82	14	2128	3	0	3	0	11
2L94_A	HIV_FE links to Rfam database...	0.92	0.85	1.00	17	973	0	0	0	0	3
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...	0.53	0.53	0.53	9	2833	12	5	3	4	8
2WWQ_V	tRNA links to Rfam database...	0.64	0.50	0.82	14	2909	4	0	3	1	14
2XKV_B	Bacteria_small_SRP links to Rfam database...	-0.01	0.00	0.00	0	4533	27	8	19	0	20
2XQD_Y	tRNA links to Rfam database...	0.86	0.74	1.00	20	2830	0	0	0	0	7
2XXA_G	Bacteria_small_SRP links to Rfam database...	-0.01	0.00	0.00	0	5122	29	1	28	0	42
2ZZM_B	tRNA links to Rfam database...	0.21	0.19	0.24	6	3461	19	0	19	0	26
2ZZN_D	tRNA links to Rfam database...	0.86	0.78	0.95	21	2463	1	0	1	0	6
3A2K_C	tRNA links to Rfam database...	0.84	0.71	1.00	20	2906	0	0	0	0	8
3A3A_A	tRNA-Sec links to Rfam database...	0.85	0.73	1.00	27	3628	0	0	0	0	10
3AKZ_H	tRNA links to Rfam database...	0.67	0.57	0.80	16	2681	5	1	3	1	12
3AMU_B	tRNA links to Rfam database...	0.64	0.56	0.75	15	2983	7	0	5	2	12
3GX2_A	SAM links to Rfam database...	0.50	0.40	0.64	16	4346	10	0	9	1	24
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...	0.29	0.29	0.29	27	60634	71	13	52	6	67
3IZ4_A	tmRNA links to Rfam database...	0.36	0.31	0.43	41	70780	59	7	48	4	91
3IZF_C	5S_rRNA links to Rfam database...	0.69	0.56	0.86	30	6868	5	0	5	0	24
3J16_L	tRNA links to Rfam database...	0.82	0.67	1.00	20	2755	0	0	0	0	10
3JYV_7	tRNA links to Rfam database...	-0.01	0.00	0.00	0	2831	19	0	19	0	32
3JYX_4	5_8S_rRNA links to Rfam database...	0.10	0.09	0.12	3	12220	33	2	21	10	30
3JYX_3	5S_rRNA links to Rfam database...	0.60	0.56	0.65	15	6305	11	4	4	3	12
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...	0.61	0.50	0.74	23	6990	9	0	8	1	23
3O58_2	5S_rRNA links to Rfam database...	0.47	0.42	0.53	16	7230	16	3	11	2	22
3O58_3	5_8S_rRNA links to Rfam database...	0.09	0.09	0.10	3	12373	35	5	22	8	32
3PDR_A	ykoK links to Rfam database...	0.57	0.44	0.74	32	12837	13	0	11	2	40
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...	0.19	0.17	0.24	7	3887	22	1	21	0	35
3UZL_B	tRNA links to Rfam database...	0.53	0.41	0.71	15	3549	6	1	5	0	22
4A1C_2	5_8S_rRNA links to Rfam database...	0.28	0.24	0.33	8	11757	28	0	16	12	25
4A1C_3	5S_rRNA links to Rfam database...	0.26	0.22	0.32	12	7103	25	2	23	0	42
4AOB_A	SAM links to Rfam database...	0.42	0.33	0.54	14	4345	13	1	11	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...	0.69	0.47	1.00	9	1317	0	0	0	0	10

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

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

Total Base Pair Counts
Total TP	243
Total TN	296923
Total FP	156
Total FP CONTRA	12
Total FP INCONS	137
Total FP COMP	7
Total FN	1270

Total Scores
MCC	0.314
Average MCC ± 95% Confidence Intervals	0.284 ± 0.100
Sensitivity	0.161
Positive Predictive Value	0.620
Nr of predictions	44

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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
2KE6_A	K10_TLS links to Rfam database...	0.83	0.74	0.93	14	1113	2	0	1	1	5
2KUR_A	K10_TLS links to Rfam database...	0.82	0.71	0.94	15	1112	1	0	1	0	6
2KUU_A	K10_TLS links to Rfam database...	0.79	0.67	0.93	14	1113	2	0	1	1	7
2KUV_A	K10_TLS links to Rfam database...	0.80	0.68	0.94	15	1112	1	0	1	0	7
2KUW_A	K10_TLS links to Rfam database...	0.73	0.62	0.87	13	1113	2	0	2	0	8
2KX8_A	7SK links to Rfam database...	0.00	0.00	0.00	0	860	1	0	1	0	18
2L1F_A	Gammaretro_CES links to Rfam database...	0.80	0.75	0.86	18	2059	3	0	3	0	6
2L1F_B	Gammaretro_CES links to Rfam database...	0.85	0.80	0.91	20	2123	2	0	2	0	5
2L94_A	HIV_FE links to Rfam database...	0.57	0.50	0.67	10	975	5	0	5	0	10
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
2XKV_B	Bacteria_small_SRP links to Rfam database...	0.28	0.20	0.40	4	4550	8	2	4	2	16
2XQD_Y	tRNA links to Rfam database...	0.00	0.00	0.00	0	2845	5	0	5	0	27
2XXA_G	Bacteria_small_SRP links to Rfam database...	0.34	0.17	0.70	7	5141	3	0	3	0	35
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
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
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

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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 Vsfold4 - scored higher in this pairwise comparison

1. Total counts & total scores for Vsfold4

2. Individual counts for Vsfold4 [ 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 ]