CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

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Overview

Metric	ProbKnot		RSpredict(seed)
MCC	0.646	>	0.425
Average MCC ± 95% Confidence Intervals	0.662 ± 0.089	>	0.175 ± 0.084
Sensitivity	0.671	>	0.286
Positive Predictive Value	0.623	<	0.634
Total TP	1043	>	445
Total TN	547241	<	548213
Total FP	872	>	336
Total FP CONTRA	200	>	51
Total FP INCONS	431	>	206
Total FP COMP	241	>	79
Total FN	511	<	1109
P-value	3.56938820447e-08

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Performance plots

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

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Performance of ProbKnot - scored higher in this pairwise comparison

1. Total counts & total scores for ProbKnot

Total Base Pair Counts
Total TP	1043
Total TN	547241
Total FP	872
Total FP CONTRA	200
Total FP INCONS	431
Total FP COMP	241
Total FN	511

Total Scores
MCC	0.646
Average MCC ± 95% Confidence Intervals	0.662 ± 0.089
Sensitivity	0.671
Positive Predictive Value	0.623
Nr of predictions	43

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

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2KX8_A	7SK links to Rfam database...	1.00	1.00	1.00	16	355	0	0	0	0	0
2L1F_A	Gammaretro_CES links to Rfam database...	1.00	1.00	1.00	23	740	0	0	0	0	0
2L1F_B	Gammaretro_CES links to Rfam database...	1.00	1.00	1.00	24	767	0	0	0	0	0
2L94_A	HIV_FE links to Rfam database...	1.00	1.00	1.00	18	339	1	0	0	1	0
2LC8_A	GP_knot1 links to Rfam database...	-0.03	0.00	0.00	0	513	15	3	12	0	18
2XKV_B	Bacteria_small_SRP links to Rfam database...	0.64	0.73	0.57	8	1821	26	0	6	20	3
2XQD_Y	tRNA links to Rfam database...	1.00	1.00	1.00	21	1108	2	0	0	2	0
2XXA_G	Bacteria_small_SRP links to Rfam database...	0.25	0.26	0.26	9	2011	26	1	24	1	26
3AKZ_H	tRNA links to Rfam database...	0.87	1.00	0.77	20	1101	9	6	0	3	0
3AMU_B	tRNA links to Rfam database...	0.77	0.79	0.75	15	1137	9	0	5	4	4
3IYQ_A	tmRNA links to Rfam database...	0.24	0.33	0.18	17	22346	97	41	36	20	34
3IZ4_A	tmRNA links to Rfam database...	0.59	0.61	0.57	58	25435	49	17	26	6	37
3IZF_C	5S_rRNA links to Rfam database...	0.90	0.91	0.89	32	2604	7	0	4	3	3
3J16_L	tRNA links to Rfam database...	0.42	0.48	0.38	10	1133	16	3	13	0	11
3J20_0	tRNA links to Rfam database...	0.54	0.57	0.52	12	1196	12	3	8	1	9
3J20_2	SSU_rRNA_archaea links to Rfam database...	0.61	0.61	0.60	253	421947	227	32	136	59	159
3J20_1	tRNA links to Rfam database...	0.75	0.75	0.75	15	1092	8	0	5	3	5
3J2L_3	5S_rRNA links to Rfam database...	0.79	0.76	0.81	26	2988	11	0	6	5	8
3J3D_C	tRNA links to Rfam database...	0.46	0.53	0.42	10	944	14	6	8	0	9
3J3E_8	5_8S_rRNA links to Rfam database...	-0.01	0.00	0.00	0	2718	37	6	18	13	15
3J3E_7	5S_rRNA links to Rfam database...	0.60	0.56	0.66	19	2712	11	1	9	1	15
3J3F_7	5S_rRNA links to Rfam database...	0.94	0.89	1.00	32	2902	3	0	0	3	4
3J3F_8	5_8S_rRNA links to Rfam database...	0.39	0.47	0.33	9	4734	38	9	9	20	10
3NPB_A	SAM links to Rfam database...	0.79	0.73	0.87	27	2247	9	0	4	5	10
3O58_3	5_8S_rRNA links to Rfam database...	0.38	0.50	0.29	11	4726	42	10	17	15	11
3O58_2	5S_rRNA links to Rfam database...	0.91	0.94	0.88	29	2721	10	0	4	6	2
3PDR_A	ykoK links to Rfam database...	0.88	0.92	0.85	46	4786	10	5	3	2	4
3RKF_A	Purine links to Rfam database...	0.87	0.83	0.91	20	844	2	2	0	0	4
3SD1_A	THF links to Rfam database...	0.66	0.69	0.65	20	1502	11	6	5	0	9
3UZL_B	tRNA links to Rfam database...	0.92	1.00	0.84	16	1274	11	3	0	8	0
3W1K_J	tRNA-Sec links to Rfam database...	0.97	0.97	0.97	30	1647	1	1	0	0	1
3W3S_B	tRNA-Sec links to Rfam database...	0.98	0.97	1.00	32	1957	1	0	0	1	1
3ZEX_C	5_8S_rRNA links to Rfam database...	0.48	0.52	0.45	15	5341	22	4	14	4	14
3ZEX_D	5S_rRNA links to Rfam database...	0.90	0.86	0.94	30	2764	7	0	2	5	5
3ZND_W	tRNA links to Rfam database...	0.24	0.38	0.16	3	1172	26	9	7	10	5
4A1C_3	5S_rRNA links to Rfam database...	0.88	0.86	0.89	32	2727	7	0	4	3	5
4A1C_2	5_8S_rRNA links to Rfam database...	0.17	0.25	0.13	5	4477	49	13	21	15	15
4AOB_A	SAM links to Rfam database...	0.60	0.59	0.63	17	1410	11	4	6	1	12
4ENB_A	crcB links to Rfam database...	0.81	0.73	0.92	11	460	1	1	0	0	4
4ENC_A	crcB links to Rfam database...	0.52	0.53	0.53	8	481	8	0	7	1	7
4FRG_B	AdoCbl-variant links to Rfam database...	0.38	0.38	0.41	9	1180	13	6	7	0	15
4FRN_A	AdoCbl-variant links to Rfam database...	0.49	0.46	0.54	13	1824	11	6	5	0	15
4JF2_A	preQ1-II links to Rfam database...	0.91	0.92	0.92	22	1058	2	2	0	0	2

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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	445
Total TN	548213
Total FP	336
Total FP CONTRA	51
Total FP INCONS	206
Total FP COMP	79
Total FN	1109

Total Scores
MCC	0.425
Average MCC ± 95% Confidence Intervals	0.175 ± 0.084
Sensitivity	0.286
Positive Predictive Value	0.634
Nr of predictions	43

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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
2KX8_A	7SK links to Rfam database...	-0.01	0.00	0.00	0	370	1	0	1	0	16
2L1F_A	Gammaretro_CES links to Rfam database...	0.81	0.78	0.86	18	742	3	0	3	0	5
2L1F_B	Gammaretro_CES links to Rfam database...	0.87	0.83	0.91	20	769	2	0	2	0	4
2L94_A	HIV_FE links to Rfam database...	0.55	0.50	0.64	9	343	6	0	5	1	9
2LC8_A	GP_knot1 links to Rfam database...	-0.03	0.00	0.00	0	515	13	0	13	0	18
2XKV_B	Bacteria_small_SRP links to Rfam database...	0.38	0.36	0.40	4	1825	8	4	2	2	7
2XQD_Y	tRNA links to Rfam database...	-0.01	0.00	0.00	0	1124	5	0	5	0	21
2XXA_G	Bacteria_small_SRP links to Rfam database...	0.37	0.20	0.70	7	2035	3	0	3	0	28
3AKZ_H	tRNA links to Rfam database...	-0.01	0.00	0.00	0	1125	2	0	2	0	20
3AMU_B	tRNA links to Rfam database...	-0.01	0.00	0.00	0	1155	2	0	2	0	19
3IYQ_A	tmRNA links to Rfam database...	0.16	0.10	0.26	5	22421	21	10	4	7	46
3IZ4_A	tmRNA links to Rfam database...	0.26	0.11	0.63	10	25520	7	2	4	1	85
3IZF_C	5S_rRNA links to Rfam database...	0.00	0.00	0.00	0	2635	5	0	5	0	35
3J16_L	tRNA links to Rfam database...	0.00	0.00	0.00	0	1158	1	0	1	0	21
3J20_0	tRNA links to Rfam database...	-0.01	0.00	0.00	0	1215	4	0	4	0	21
3J20_2	SSU_rRNA_archaea links to Rfam database...	0.77	0.76	0.78	312	421966	152	18	72	62	100
3J20_1	tRNA links to Rfam database...	-0.01	0.00	0.00	0	1108	5	0	4	1	20
3J2L_3	5S_rRNA links to Rfam database...	0.00	0.00	0.00	0	3015	5	0	5	0	34
3J3D_C	tRNA links to Rfam database...	-0.01	0.00	0.00	0	964	4	1	3	0	19
3J3E_8	5_8S_rRNA links to Rfam database...	0.00	0.00	0.00	0	2742	0	0	0	0	15
3J3E_7	5S_rRNA links to Rfam database...	-0.01	0.00	0.00	0	2733	8	1	7	0	34
3J3F_7	5S_rRNA links to Rfam database...	0.00	0.00	0.00	0	2930	4	1	3	0	36
3J3F_8	5_8S_rRNA links to Rfam database...	0.19	0.11	0.33	2	4755	5	3	1	1	17
3NPB_A	SAM links to Rfam database...	-0.01	0.00	0.00	0	2274	4	0	4	0	37
3O58_3	5_8S_rRNA links to Rfam database...	0.28	0.14	0.60	3	4759	2	0	2	0	19
3O58_2	5S_rRNA links to Rfam database...	0.00	0.00	0.00	0	2751	3	0	3	0	31
3PDR_A	ykoK links to Rfam database...	0.00	0.00	0.00	0	4832	8	0	8	0	50
3RKF_A	Purine links to Rfam database...	0.84	0.75	0.95	18	847	1	1	0	0	6
3SD1_A	THF links to Rfam database...	0.00	0.00	0.00	0	1533	0	0	0	0	29
3UZL_B	tRNA links to Rfam database...	-0.01	0.00	0.00	0	1287	6	3	3	0	16
3W1K_J	tRNA-Sec links to Rfam database...	0.57	0.35	0.92	11	1666	1	0	1	0	20
3W3S_B	tRNA-Sec links to Rfam database...	0.45	0.36	0.57	12	1968	10	1	8	1	21
3ZEX_C	5_8S_rRNA links to Rfam database...	0.13	0.07	0.25	2	5366	6	2	4	0	27
3ZEX_D	5S_rRNA links to Rfam database...	0.00	0.00	0.00	0	2794	2	0	2	0	35
3ZND_W	tRNA links to Rfam database...	0.00	0.00	0.00	0	1189	4	0	2	2	8
4A1C_3	5S_rRNA links to Rfam database...	0.00	0.00	0.00	0	2759	4	2	2	0	37
4A1C_2	5_8S_rRNA links to Rfam database...	0.00	0.00	0.00	0	4512	5	2	2	1	20
4AOB_A	SAM links to Rfam database...	0.42	0.21	0.86	6	1430	1	0	1	0	23
4ENB_A	crcB links to Rfam database...	0.34	0.20	0.60	3	467	2	0	2	0	12
4ENC_A	crcB links to Rfam database...	0.34	0.20	0.60	3	491	2	0	2	0	12
4FRG_B	AdoCbl-variant links to Rfam database...	-0.01	0.00	0.00	0	1200	2	0	2	0	24
4FRN_A	AdoCbl-variant links to Rfam database...	0.00	0.00	0.00	0	1845	3	0	3	0	28
4JF2_A	preQ1-II links to Rfam database...	-0.01	0.00	0.00	0	1078	4	0	4	0	24

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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 ProbKnot - scored higher in this pairwise comparison

1. Total counts & total scores for ProbKnot

2. Individual counts for ProbKnot [ 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 ]