CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

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Overview

Metric	McQFold		RSpredict(seed)
MCC	0.531	>	0.375
Average MCC ± 95% Confidence Intervals	0.602 ± 0.074	>	0.235 ± 0.079
Sensitivity	0.462	>	0.220
Positive Predictive Value	0.613	<	0.642
Total TP	1272	>	606
Total TN	1507226	<	1508357
Total FP	889	>	351
Total FP CONTRA	98	>	25
Total FP INCONS	705	>	313
Total FP COMP	86	>	13
Total FN	1482	<	2148
P-value	3.56938820447e-08

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Performance plots

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

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Performance of McQFold - scored higher in this pairwise comparison

1. Total counts & total scores for McQFold

Total Base Pair Counts
Total TP	1272
Total TN	1507226
Total FP	889
Total FP CONTRA	98
Total FP INCONS	705
Total FP COMP	86
Total FN	1482

Total Scores
MCC	0.531
Average MCC ± 95% Confidence Intervals	0.602 ± 0.074
Sensitivity	0.462
Positive Predictive Value	0.613
Nr of predictions	61

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2. Individual counts for McQFold [ 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...	0.89	0.79	1.00	15	1113	1	0	0	1	4
2KUR_A	K10_TLS links to Rfam database...	0.87	0.76	1.00	16	1112	0	0	0	0	5
2KUU_A	K10_TLS links to Rfam database...	0.84	0.71	1.00	15	1113	1	0	0	1	6
2KUV_A	K10_TLS links to Rfam database...	0.85	0.73	1.00	16	1112	0	0	0	0	6
2KUW_A	K10_TLS links to Rfam database...	0.87	0.76	1.00	16	1112	0	0	0	0	5
2KX8_A	7SK links to Rfam database...	0.88	0.83	0.94	15	845	1	0	1	0	3
2L1F_A	Gammaretro_CES links to Rfam database...	0.98	0.96	1.00	23	2057	0	0	0	0	1
2L1F_B	Gammaretro_CES links to Rfam database...	0.98	0.96	1.00	24	2121	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...	0.61	0.55	0.69	11	1524	5	0	5	0	9
2WRQ_Y	tRNA links to Rfam database...	0.57	0.59	0.56	10	2832	13	5	3	5	7
2WWQ_V	tRNA links to Rfam database...	0.00	0.00	0.00	0	2926	0	0	0	0	28
2XKV_B	Bacteria_small_SRP links to Rfam database...	0.31	0.30	0.33	6	4542	25	1	11	13	14
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...	0.27	0.24	0.32	10	5120	21	0	21	0	32
2ZZM_B	tRNA links to Rfam database...	0.21	0.19	0.24	6	3461	19	2	17	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...	0.86	0.75	1.00	21	2905	0	0	0	0	7
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...	0.68	0.61	0.77	17	2679	6	1	4	1	11
3AMU_B	tRNA links to Rfam database...	0.75	0.59	0.94	16	2986	3	0	1	2	11
3GX2_A	SAM links to Rfam database...	0.47	0.40	0.57	16	4343	13	1	11	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...	0.28	0.31	0.26	29	60614	87	19	64	4	65
3IZ4_A	tmRNA links to Rfam database...	0.42	0.36	0.49	47	70780	53	6	43	4	85
3IZF_C	5S_rRNA links to Rfam database...	0.68	0.56	0.83	30	6867	6	0	6	0	24
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...	0.66	0.57	0.77	17	2828	6	1	4	1	13
3J20_2	SSU_rRNA_archaea links to Rfam database...	0.46	0.39	0.54	249	1116304	216	8	204	4	384
3J2L_3	5S_rRNA links to Rfam database...	0.56	0.43	0.72	23	7843	11	0	9	2	30
3J3D_C	tRNA links to Rfam database...	0.82	0.71	0.95	20	2754	1	0	1	0	8
3J3E_8	5_8S_rRNA links to Rfam database...	0.00	0.00	0.00	0	7479	36	3	21	12	33
3J3E_7	5S_rRNA links to Rfam database...	0.46	0.37	0.59	20	7106	14	1	13	0	34
3J3F_7	5S_rRNA links to Rfam database...	0.18	0.16	0.22	8	7223	29	1	28	0	42
3J3F_8	5_8S_rRNA links to Rfam database...	0.30	0.31	0.30	11	12209	38	4	22	12	25
3JYV_7	tRNA links to Rfam database...	-0.01	0.00	0.00	0	2830	20	0	20	0	32
3JYX_3	5S_rRNA links to Rfam database...	0.21	0.22	0.20	6	6298	24	9	15	0	21
3JYX_4	5_8S_rRNA links to Rfam database...	0.20	0.21	0.19	7	12210	33	8	21	4	26
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...	0.81	0.67	0.97	31	6989	4	1	0	3	15
3O58_3	5_8S_rRNA links to Rfam database...	0.26	0.26	0.26	9	12368	26	10	16	0	26
3O58_2	5S_rRNA links to Rfam database...	0.83	0.71	0.96	27	7232	2	0	1	1	11
3PDR_A	ykoK links to Rfam database...	0.69	0.56	0.87	40	12834	9	0	6	3	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...	0.71	0.60	0.86	25	3887	4	0	4	0	17
3UZL_B	tRNA links to Rfam database...	0.45	0.41	0.52	15	3541	14	0	14	0	22
3W1K_J	tRNA-Sec links to Rfam database...	0.78	0.63	0.96	24	4161	1	1	0	0	14
3W3S_B	tRNA-Sec links to Rfam database...	0.44	0.38	0.54	15	4725	14	0	13	1	25
3ZEX_C	5_8S_rRNA links to Rfam database...	0.27	0.21	0.34	11	14164	24	2	19	3	41
3ZEX_D	5S_rRNA links to Rfam database...	0.69	0.53	0.90	26	6992	3	1	2	0	23
3ZND_W	tRNA links to Rfam database...	0.20	0.22	0.19	5	2977	23	1	20	2	18
4A1C_2	5_8S_rRNA links to Rfam database...	0.15	0.15	0.15	5	11748	33	5	23	5	28
4A1C_3	5S_rRNA links to Rfam database...	0.25	0.22	0.29	12	7099	29	1	28	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...	0.89	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...	0.81	0.66	1.00	21	3465	0	0	0	0	11
4FRN_A	AdoCbl-variant links to Rfam database...	0.73	0.56	0.95	20	5130	1	1	0	0	16
4JF2_A	preQ1-II links to Rfam database...	0.83	0.81	0.86	25	2821	4	3	1	0	6

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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	606
Total TN	1508357
Total FP	351
Total FP CONTRA	25
Total FP INCONS	313
Total FP COMP	13
Total FN	2148

Total Scores
MCC	0.375
Average MCC ± 95% Confidence Intervals	0.235 ± 0.079
Sensitivity	0.220
Positive Predictive Value	0.642
Nr of predictions	61

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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
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_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_7	5S_rRNA links to Rfam database...	0.00	0.00	0.00	0	7256	4	0	4	0	50
3J3F_8	5_8S_rRNA links to Rfam database...	0.14	0.06	0.33	2	12240	5	1	3	1	34
3JYV_7	tRNA links to Rfam database...	0.00	0.00	0.00	0	2846	4	0	4	0	32
3JYX_3	5S_rRNA links to Rfam database...	0.00	0.00	0.00	0	6323	5	1	4	0	27
3JYX_4	5_8S_rRNA links to Rfam database...	0.00	0.00	0.00	0	12241	5	0	5	0	33
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_3	5_8S_rRNA links to Rfam database...	0.23	0.09	0.60	3	12398	2	0	2	0	32
3O58_2	5S_rRNA links to Rfam database...	0.00	0.00	0.00	0	7257	3	0	3	0	38
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_C	5_8S_rRNA links to Rfam database...	0.10	0.04	0.25	2	14188	6	1	5	0	50
3ZEX_D	5S_rRNA links to Rfam database...	0.00	0.00	0.00	0	7019	2	0	2	0	49
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

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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 McQFold - scored higher in this pairwise comparison

1. Total counts & total scores for McQFold

2. Individual counts for McQFold [ 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 ]