CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

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Overview

Metric	PknotsRG		RSpredict(seed)
MCC	0.588	>	0.266
Average MCC ± 95% Confidence Intervals	0.628 ± 0.065	>	0.228 ± 0.079
Sensitivity	0.533	>	0.128
Positive Predictive Value	0.653	>	0.561
Total TP	1130	>	271
Total TN	390805	<	392053
Total FP	722	>	222
Total FP CONTRA	88	>	16
Total FP INCONS	513	>	196
Total FP COMP	121	>	10
Total FN	991	<	1850
P-value	3.56938820447e-08

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Performance plots

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

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Performance of PknotsRG - scored higher in this pairwise comparison

1. Total counts & total scores for PknotsRG

Total Base Pair Counts
Total TP	1130
Total TN	390805
Total FP	722
Total FP CONTRA	88
Total FP INCONS	513
Total FP COMP	121
Total FN	991

Total Scores
MCC	0.588
Average MCC ± 95% Confidence Intervals	0.628 ± 0.065
Sensitivity	0.533
Positive Predictive Value	0.653
Nr of predictions	60

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2. Individual counts for PknotsRG [ 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...	0.86	0.84	0.89	16	1110	3	0	2	1	3
2KUR_A	K10_TLS links to Rfam database...	0.85	0.81	0.89	17	1109	2	0	2	0	4
2KUU_A	K10_TLS links to Rfam database...	0.82	0.76	0.89	16	1110	3	0	2	1	5
2KUV_A	K10_TLS links to Rfam database...	0.83	0.77	0.89	17	1109	2	0	2	0	5
2KUW_A	K10_TLS links to Rfam database...	0.90	0.86	0.95	18	1109	1	0	1	0	3
2KX8_A	7SK links to Rfam database...	0.94	0.89	1.00	16	845	0	0	0	0	2
2L1F_B	Gammaretro_CES links to Rfam database...	0.98	0.96	1.00	24	2121	0	0	0	0	1
2L1F_A	Gammaretro_CES links to Rfam database...	0.98	0.96	1.00	23	2057	0	0	0	0	1
2L94_A	HIV_FE links to Rfam database...	0.97	0.95	1.00	19	971	0	0	0	0	1
2LC8_A	GP_knot1 links to Rfam database...	0.63	0.55	0.73	11	1525	4	1	3	0	9
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...	0.76	0.68	0.86	19	2904	5	0	3	2	9
2XKV_B	Bacteria_small_SRP links to Rfam database...	0.51	0.50	0.53	10	4541	22	0	9	13	10
2XQD_Y	tRNA links to Rfam database...	0.88	0.78	1.00	21	2829	0	0	0	0	6
2XXA_G	Bacteria_small_SRP links to Rfam database...	0.34	0.31	0.39	13	5118	20	1	19	0	29
2ZZM_B	tRNA links to Rfam database...	0.21	0.19	0.25	6	3462	18	0	18	0	26
2ZZN_D	tRNA links to Rfam database...	0.84	0.78	0.91	21	2462	2	0	2	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...	0.41	0.39	0.44	11	2676	14	4	10	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...	0.67	0.55	0.81	22	4344	6	0	5	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...	0.31	0.33	0.28	31	60617	80	24	54	2	63
3IZ4_A	tmRNA links to Rfam database...	0.51	0.47	0.55	62	70763	52	10	41	1	70
3IZF_C	5S_rRNA links to Rfam database...	0.59	0.52	0.67	28	6861	14	1	13	0	26
3J16_L	tRNA links to Rfam database...	0.75	0.57	1.00	17	2758	0	0	0	0	13
3J20_1	tRNA links to Rfam database...	0.96	0.91	1.00	21	2905	0	0	0	0	2
3J20_0	tRNA links to Rfam database...	0.43	0.40	0.48	12	2825	14	0	13	1	18
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...	0.60	0.54	0.68	15	2753	7	0	7	0	13
3J3E_8	5_8S_rRNA links to Rfam database...	0.17	0.15	0.19	5	7477	30	2	19	9	28
3J3E_7	5S_rRNA links to Rfam database...	0.58	0.48	0.70	26	7103	11	1	10	0	28
3J3F_8	5_8S_rRNA links to Rfam database...	0.31	0.31	0.31	11	12211	37	4	20	13	25
3J3F_7	5S_rRNA links to Rfam database...	0.80	0.70	0.92	35	7222	4	0	3	1	15
3JYV_7	tRNA links to Rfam database...	-0.01	0.00	0.00	0	2828	22	1	21	0	32
3JYX_4	5_8S_rRNA links to Rfam database...	0.31	0.30	0.32	10	12215	33	5	16	12	23
3JYX_3	5S_rRNA links to Rfam database...	0.62	0.63	0.61	17	6300	22	1	10	11	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...	0.83	0.72	0.97	33	6987	3	0	1	2	13
3O58_2	5S_rRNA links to Rfam database...	0.59	0.61	0.58	23	7220	19	4	13	2	15
3O58_3	5_8S_rRNA links to Rfam database...	0.34	0.34	0.34	12	12368	34	2	21	11	23
3PDR_A	ykoK links to Rfam database...	0.75	0.63	0.90	45	12830	7	1	4	2	27
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...	0.61	0.50	0.75	21	3888	7	1	6	0	21
3UZL_B	tRNA links to Rfam database...	0.48	0.38	0.61	14	3547	9	0	9	0	23
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...	0.58	0.53	0.66	21	4721	12	1	10	1	19
3ZEX_D	5S_rRNA links to Rfam database...	0.77	0.65	0.91	32	6986	3	0	3	0	17
3ZEX_C	5_8S_rRNA links to Rfam database...	0.24	0.21	0.28	11	14157	43	1	27	15	41
3ZND_W	tRNA links to Rfam database...	0.20	0.22	0.19	5	2977	22	1	20	1	18
4A1C_3	5S_rRNA links to Rfam database...	0.70	0.59	0.82	32	7101	7	1	6	0	22
4A1C_2	5_8S_rRNA links to Rfam database...	0.14	0.15	0.13	5	11742	43	5	29	9	28
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...	0.89	0.79	1.00	15	1260	0	0	0	0	4
4ENC_A	crcB links to Rfam database...	0.86	0.79	0.94	15	1310	1	1	0	0	4
4FRG_B	AdoCbl-variant links to Rfam database...	0.32	0.28	0.38	9	3462	15	0	15	0	23
4FRN_A	AdoCbl-variant links to Rfam database...	0.52	0.44	0.62	16	5125	10	2	8	0	20
4JF2_A	preQ1-II links to Rfam database...	0.77	0.71	0.85	22	2824	4	3	1	0	9

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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	271
Total TN	392053
Total FP	222
Total FP CONTRA	16
Total FP INCONS	196
Total FP COMP	10
Total FN	1850

Total Scores
MCC	0.266
Average MCC ± 95% Confidence Intervals	0.228 ± 0.079
Sensitivity	0.128
Positive Predictive Value	0.561
Nr of predictions	60

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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_B	Gammaretro_CES links to Rfam database...	0.85	0.80	0.91	20	2123	2	0	2	0	5
2L1F_A	Gammaretro_CES links to Rfam database...	0.80	0.75	0.86	18	2059	3	0	3	0	6
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
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
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_8	5_8S_rRNA links to Rfam database...	0.00	0.00	0.00	0	7503	0	0	0	0	33
3J3E_7	5S_rRNA links to Rfam database...	0.00	0.00	0.00	0	7132	8	0	8	0	54
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_3	5S_rRNA links to Rfam database...	0.00	0.00	0.00	0	7136	4	1	3	0	54
4A1C_2	5_8S_rRNA links to Rfam database...	0.00	0.00	0.00	0	11777	5	1	3	1	33
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

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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 PknotsRG - scored higher in this pairwise comparison

1. Total counts & total scores for PknotsRG

2. Individual counts for PknotsRG [ 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 ]